to get rid of warning and error: non-language object in R
0
I am coding in R and I have a small chunk that I need to loop it over.
the part of the code looks like this:
sc_1$ue <- cF(sc_1, 2500, 1000, 5)
sc_2$ue <- cF(sc_2, 2500, 1000, 5)
sc_3$ue <- cF(sc_3, 2500, 1000, 5)
sc_4$ue <- cF(sc_4, 3000, 1000, 5)
where cF is a function I am calling. This code in its present form works without any error.
However, when I try to loop it like the following:
sc_list=mget(sc)
for (i in 1:5)
sc_list[i]$ue <- cF(sc_list[i], 2500, 1000, 5)
where sc contains sc_1 to sc_n objects.
The output is not an immediate error but a warning.
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
because of this following code in the program gives me an error.
How can I fix this?
What I have tried is:
sc_list=mget(sc)
for (i in 1:length(paths))
paste0("sc_",i)$ue <- cF(sc_list[i], 2500, 1000, 5)
This throws up an error.
Quitting from lines 209-217 (prototype.Rmd)
Error in paste0("sc_", i)$use <- cF(sc_list[i], 2500, 1000, :
target of assignment expands to non-language object
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted
Edit: output of
> str(sc_list)
List of 4
$ sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots
.. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData :List of 2
.. .. .. .. ..$ is_spike_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. ..$ is_spike : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_metadata :List of 2
.. .. ..$ version :Classes 'package_version', 'numeric_version' hidden list of 1
.. .. .. ..$ : int [1:3] 1 0 0
.. .. ..$ spike_names: chr "MT"
.. ..@ reducedDims :Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
.. .. .. ..@ listData : list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ rowRanges :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots
.. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
.. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 0 levels:
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*":
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. .. .. ..@ nrows : int 0
.. .. .. .. .. .. .. ..@ listData : Named list()
.. .. .. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. .. .. ..@ seqnames : chr(0)
.. .. .. .. .. .. .. ..@ seqlengths : int(0)
.. .. .. .. .. .. .. ..@ is_circular: logi(0)
.. .. .. .. .. .. .. ..@ genome : chr(0)
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 33694
.. .. .. .. .. ..@ listData :List of 11
.. .. .. .. .. .. ..$ id : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. .. ..$ symbol : chr [1:33694] "RP11-34P13.3" "FAM138A" "OR4F5" "RP11-34P13.7" ...
.. .. .. .. .. .. ..$ is_feature_control : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ is_feature_control_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ mean_counts : num [1:33694] 0 0 0 0.000895 0.000179 ...
.. .. .. .. .. .. ..$ log10_mean_counts : num [1:33694] 0.00 0.00 0.00 3.89e-04 7.77e-05 ...
.. .. .. .. .. .. ..$ rank_counts : num [1:33694] 6741 6741 6741 18054 14520 ...
.. .. .. .. .. .. ..$ n_cells_counts : int [1:33694] 0 0 0 5 1 0 0 0 611 542 ...
.. .. .. .. .. .. ..$ pct_dropout_counts : num [1:33694] 100 100 100 99.9 100 ...
.. .. .. .. .. .. ..$ total_counts : num [1:33694] 0 0 0 5 1 0 0 0 661 617 ...
.. .. .. .. .. .. ..$ log10_total_counts : num [1:33694] 0 0 0 0.778 0.301 ...
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:33694] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. .. ..@ NAMES : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementType : chr "GRanges"
.. .. .. ..@ metadata : list()
.. ..@ colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData :List of 30
.. .. .. .. ..$ dataset : int [1:5586] 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..$ barcode : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. .. ..$ total_features : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_top_50_features : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features : num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features : num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features : num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_endogenous : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features_endogenous : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts_endogenous : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts_endogenous : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_endogenous : num [1:5586] 100 100 100 100 100 100 100 100 100 100 ...
.. .. .. .. ..$ pct_counts_top_50_features_endogenous : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features_endogenous: num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features_endogenous: num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features_endogenous: num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_feature_control : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_features_MT : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ is_cell_control : logi [1:5586] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ assays :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field
.. .. ..$ data: NULL
.. .. ..and 14 methods.
.. ..@ NAMES : NULL
.. ..@ elementMetadata :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ metadata :List of 1
.. .. ..$ name: chr "iMates-1"
Here is one of the four objects.
Could anyone of you help me.
Thank you
r s4
asked Nov 22 '18 at 15:25
user1826775user1826775
33
|
show 2 more comments
0
I am coding in R and I have a small chunk that I need to loop it over.
the part of the code looks like this:
sc_1$ue <- cF(sc_1, 2500, 1000, 5)
sc_2$ue <- cF(sc_2, 2500, 1000, 5)
sc_3$ue <- cF(sc_3, 2500, 1000, 5)
sc_4$ue <- cF(sc_4, 3000, 1000, 5)
where cF is a function I am calling. This code in its present form works without any error.
However, when I try to loop it like the following:
sc_list=mget(sc)
for (i in 1:5)
sc_list[i]$ue <- cF(sc_list[i], 2500, 1000, 5)
where sc contains sc_1 to sc_n objects.
The output is not an immediate error but a warning.
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
because of this following code in the program gives me an error.
How can I fix this?
What I have tried is:
sc_list=mget(sc)
for (i in 1:length(paths))
paste0("sc_",i)$ue <- cF(sc_list[i], 2500, 1000, 5)
This throws up an error.
Quitting from lines 209-217 (prototype.Rmd)
Error in paste0("sc_", i)$use <- cF(sc_list[i], 2500, 1000, :
target of assignment expands to non-language object
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted
Edit: output of
> str(sc_list)
List of 4
$ sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots
.. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData :List of 2
.. .. .. .. ..$ is_spike_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. ..$ is_spike : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_metadata :List of 2
.. .. ..$ version :Classes 'package_version', 'numeric_version' hidden list of 1
.. .. .. ..$ : int [1:3] 1 0 0
.. .. ..$ spike_names: chr "MT"
.. ..@ reducedDims :Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
.. .. .. ..@ listData : list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ rowRanges :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots
.. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
.. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 0 levels:
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*":
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. .. .. ..@ nrows : int 0
.. .. .. .. .. .. .. ..@ listData : Named list()
.. .. .. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. .. .. ..@ seqnames : chr(0)
.. .. .. .. .. .. .. ..@ seqlengths : int(0)
.. .. .. .. .. .. .. ..@ is_circular: logi(0)
.. .. .. .. .. .. .. ..@ genome : chr(0)
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 33694
.. .. .. .. .. ..@ listData :List of 11
.. .. .. .. .. .. ..$ id : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. .. ..$ symbol : chr [1:33694] "RP11-34P13.3" "FAM138A" "OR4F5" "RP11-34P13.7" ...
.. .. .. .. .. .. ..$ is_feature_control : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ is_feature_control_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ mean_counts : num [1:33694] 0 0 0 0.000895 0.000179 ...
.. .. .. .. .. .. ..$ log10_mean_counts : num [1:33694] 0.00 0.00 0.00 3.89e-04 7.77e-05 ...
.. .. .. .. .. .. ..$ rank_counts : num [1:33694] 6741 6741 6741 18054 14520 ...
.. .. .. .. .. .. ..$ n_cells_counts : int [1:33694] 0 0 0 5 1 0 0 0 611 542 ...
.. .. .. .. .. .. ..$ pct_dropout_counts : num [1:33694] 100 100 100 99.9 100 ...
.. .. .. .. .. .. ..$ total_counts : num [1:33694] 0 0 0 5 1 0 0 0 661 617 ...
.. .. .. .. .. .. ..$ log10_total_counts : num [1:33694] 0 0 0 0.778 0.301 ...
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:33694] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. .. ..@ NAMES : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementType : chr "GRanges"
.. .. .. ..@ metadata : list()
.. ..@ colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData :List of 30
.. .. .. .. ..$ dataset : int [1:5586] 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..$ barcode : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. .. ..$ total_features : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_top_50_features : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features : num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features : num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features : num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_endogenous : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features_endogenous : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts_endogenous : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts_endogenous : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_endogenous : num [1:5586] 100 100 100 100 100 100 100 100 100 100 ...
.. .. .. .. ..$ pct_counts_top_50_features_endogenous : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features_endogenous: num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features_endogenous: num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features_endogenous: num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_feature_control : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_features_MT : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ is_cell_control : logi [1:5586] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ assays :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field
.. .. ..$ data: NULL
.. .. ..and 14 methods.
.. ..@ NAMES : NULL
.. ..@ elementMetadata :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ metadata :List of 1
.. .. ..$ name: chr "iMates-1"
Here is one of the four objects.
Could anyone of you help me.
Thank you
r s4
asked Nov 22 '18 at 15:25
user1826775user1826775
33
1
are you sure your sc_list contains anything? I'm not suremgetworks that way...
– iod
Nov 22 '18 at 15:32
It is not empty.
– user1826775
Nov 22 '18 at 15:57
Please put the additional information aboutstr(sc_list)from the comment in your question, i.e. edit your question: stackoverflow.com/posts/53434082/edit
– jogo
Nov 22 '18 at 18:44
@jogo edited the question. Please have a look.
– user1826775
Nov 22 '18 at 20:47
The objectsc_listis a list of S4-objects. The components of a S4-object are slots. The operator to access a slot is@(not$).
– jogo
Nov 22 '18 at 23:02
|
show 2 more comments
0
0
0
I am coding in R and I have a small chunk that I need to loop it over.
the part of the code looks like this:
sc_1$ue <- cF(sc_1, 2500, 1000, 5)
sc_2$ue <- cF(sc_2, 2500, 1000, 5)
sc_3$ue <- cF(sc_3, 2500, 1000, 5)
sc_4$ue <- cF(sc_4, 3000, 1000, 5)
where cF is a function I am calling. This code in its present form works without any error.
However, when I try to loop it like the following:
sc_list=mget(sc)
for (i in 1:5)
sc_list[i]$ue <- cF(sc_list[i], 2500, 1000, 5)
where sc contains sc_1 to sc_n objects.
The output is not an immediate error but a warning.
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
because of this following code in the program gives me an error.
How can I fix this?
What I have tried is:
sc_list=mget(sc)
for (i in 1:length(paths))
paste0("sc_",i)$ue <- cF(sc_list[i], 2500, 1000, 5)
This throws up an error.
Quitting from lines 209-217 (prototype.Rmd)
Error in paste0("sc_", i)$use <- cF(sc_list[i], 2500, 1000, :
target of assignment expands to non-language object
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted
Edit: output of
> str(sc_list)
List of 4
$ sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots
.. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData :List of 2
.. .. .. .. ..$ is_spike_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. ..$ is_spike : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_metadata :List of 2
.. .. ..$ version :Classes 'package_version', 'numeric_version' hidden list of 1
.. .. .. ..$ : int [1:3] 1 0 0
.. .. ..$ spike_names: chr "MT"
.. ..@ reducedDims :Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
.. .. .. ..@ listData : list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ rowRanges :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots
.. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
.. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 0 levels:
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*":
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. .. .. ..@ nrows : int 0
.. .. .. .. .. .. .. ..@ listData : Named list()
.. .. .. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. .. .. ..@ seqnames : chr(0)
.. .. .. .. .. .. .. ..@ seqlengths : int(0)
.. .. .. .. .. .. .. ..@ is_circular: logi(0)
.. .. .. .. .. .. .. ..@ genome : chr(0)
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 33694
.. .. .. .. .. ..@ listData :List of 11
.. .. .. .. .. .. ..$ id : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. .. ..$ symbol : chr [1:33694] "RP11-34P13.3" "FAM138A" "OR4F5" "RP11-34P13.7" ...
.. .. .. .. .. .. ..$ is_feature_control : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ is_feature_control_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ mean_counts : num [1:33694] 0 0 0 0.000895 0.000179 ...
.. .. .. .. .. .. ..$ log10_mean_counts : num [1:33694] 0.00 0.00 0.00 3.89e-04 7.77e-05 ...
.. .. .. .. .. .. ..$ rank_counts : num [1:33694] 6741 6741 6741 18054 14520 ...
.. .. .. .. .. .. ..$ n_cells_counts : int [1:33694] 0 0 0 5 1 0 0 0 611 542 ...
.. .. .. .. .. .. ..$ pct_dropout_counts : num [1:33694] 100 100 100 99.9 100 ...
.. .. .. .. .. .. ..$ total_counts : num [1:33694] 0 0 0 5 1 0 0 0 661 617 ...
.. .. .. .. .. .. ..$ log10_total_counts : num [1:33694] 0 0 0 0.778 0.301 ...
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:33694] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. .. ..@ NAMES : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementType : chr "GRanges"
.. .. .. ..@ metadata : list()
.. ..@ colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData :List of 30
.. .. .. .. ..$ dataset : int [1:5586] 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..$ barcode : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. .. ..$ total_features : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_top_50_features : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features : num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features : num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features : num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_endogenous : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features_endogenous : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts_endogenous : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts_endogenous : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_endogenous : num [1:5586] 100 100 100 100 100 100 100 100 100 100 ...
.. .. .. .. ..$ pct_counts_top_50_features_endogenous : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features_endogenous: num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features_endogenous: num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features_endogenous: num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_feature_control : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_features_MT : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ is_cell_control : logi [1:5586] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ assays :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field
.. .. ..$ data: NULL
.. .. ..and 14 methods.
.. ..@ NAMES : NULL
.. ..@ elementMetadata :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ metadata :List of 1
.. .. ..$ name: chr "iMates-1"
Here is one of the four objects.
Could anyone of you help me.
Thank you
r s4
asked Nov 22 '18 at 15:25
user1826775user1826775
33
I am coding in R and I have a small chunk that I need to loop it over.
the part of the code looks like this:
sc_1$ue <- cF(sc_1, 2500, 1000, 5)
sc_2$ue <- cF(sc_2, 2500, 1000, 5)
sc_3$ue <- cF(sc_3, 2500, 1000, 5)
sc_4$ue <- cF(sc_4, 3000, 1000, 5)
where cF is a function I am calling. This code in its present form works without any error.
However, when I try to loop it like the following:
sc_list=mget(sc)
for (i in 1:5)
sc_list[i]$ue <- cF(sc_list[i], 2500, 1000, 5)
where sc contains sc_1 to sc_n objects.
The output is not an immediate error but a warning.
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
## Warning in sc_list[i] <- `*vtmp*`: number of items to replace is not a
## multiple of replacement length
because of this following code in the program gives me an error.
How can I fix this?
What I have tried is:
sc_list=mget(sc)
for (i in 1:length(paths))
paste0("sc_",i)$ue <- cF(sc_list[i], 2500, 1000, 5)
This throws up an error.
Quitting from lines 209-217 (prototype.Rmd)
Error in paste0("sc_", i)$use <- cF(sc_list[i], 2500, 1000, :
target of assignment expands to non-language object
Calls: <Anonymous> ... handle -> withCallingHandlers -> withVisible -> eval -> eval
Execution halted
Edit: output of
> str(sc_list)
List of 4
$ sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots
.. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData :List of 2
.. .. .. .. ..$ is_spike_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. ..$ is_spike : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ int_metadata :List of 2
.. .. ..$ version :Classes 'package_version', 'numeric_version' hidden list of 1
.. .. .. ..$ : int [1:3] 1 0 0
.. .. ..$ spike_names: chr "MT"
.. ..@ reducedDims :Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
.. .. .. ..@ listData : list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ rowRanges :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots
.. .. .. ..@ unlistData :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
.. .. .. .. .. ..@ seqnames :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 0 levels:
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ ranges :Formal class 'IRanges' [package "IRanges"] with 6 slots
.. .. .. .. .. .. .. ..@ start : int(0)
.. .. .. .. .. .. .. ..@ width : int(0)
.. .. .. .. .. .. .. ..@ NAMES : NULL
.. .. .. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ strand :Formal class 'Rle' [package "S4Vectors"] with 4 slots
.. .. .. .. .. .. .. ..@ values : Factor w/ 3 levels "+","-","*":
.. .. .. .. .. .. .. ..@ lengths : int(0)
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. .. .. ..@ nrows : int 0
.. .. .. .. .. .. .. ..@ listData : Named list()
.. .. .. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. .. .. ..@ metadata : list()
.. .. .. .. .. ..@ seqinfo :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
.. .. .. .. .. .. .. ..@ seqnames : chr(0)
.. .. .. .. .. .. .. ..@ seqlengths : int(0)
.. .. .. .. .. .. .. ..@ is_circular: logi(0)
.. .. .. .. .. .. .. ..@ genome : chr(0)
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. .. .. ..@ rownames : NULL
.. .. .. .. .. ..@ nrows : int 33694
.. .. .. .. .. ..@ listData :List of 11
.. .. .. .. .. .. ..$ id : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. .. ..$ symbol : chr [1:33694] "RP11-34P13.3" "FAM138A" "OR4F5" "RP11-34P13.7" ...
.. .. .. .. .. .. ..$ is_feature_control : logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ is_feature_control_MT: logi [1:33694] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. .. .. .. ..$ mean_counts : num [1:33694] 0 0 0 0.000895 0.000179 ...
.. .. .. .. .. .. ..$ log10_mean_counts : num [1:33694] 0.00 0.00 0.00 3.89e-04 7.77e-05 ...
.. .. .. .. .. .. ..$ rank_counts : num [1:33694] 6741 6741 6741 18054 14520 ...
.. .. .. .. .. .. ..$ n_cells_counts : int [1:33694] 0 0 0 5 1 0 0 0 611 542 ...
.. .. .. .. .. .. ..$ pct_dropout_counts : num [1:33694] 100 100 100 99.9 100 ...
.. .. .. .. .. .. ..$ total_counts : num [1:33694] 0 0 0 5 1 0 0 0 661 617 ...
.. .. .. .. .. .. ..$ log10_total_counts : num [1:33694] 0 0 0 0.778 0.301 ...
.. .. .. .. .. ..@ elementType : chr "ANY"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ partitioning :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
.. .. .. .. .. ..@ end : int [1:33694] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. .. ..@ NAMES : chr [1:33694] "ENSG00000243485" "ENSG00000237613" "ENSG00000186092" "ENSG00000238009" ...
.. .. .. .. .. ..@ elementType : chr "integer"
.. .. .. .. .. ..@ elementMetadata: NULL
.. .. .. .. .. ..@ metadata : list()
.. .. .. ..@ elementType : chr "GRanges"
.. .. .. ..@ metadata : list()
.. ..@ colData :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. ..@ nrows : int 5586
.. .. .. ..@ listData :List of 30
.. .. .. .. ..$ dataset : int [1:5586] 1 1 1 1 1 1 1 1 1 1 ...
.. .. .. .. ..$ barcode : chr [1:5586] "AAACCTGAGAAGGTTT-1" "AAACCTGAGCGTTCCG-1" "AAACCTGAGTACGTAA-1" "AAACCTGGTAAACACA-1" ...
.. .. .. .. ..$ total_features : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_top_50_features : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features : num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features : num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features : num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_endogenous : int [1:5586] 1373 1837 2259 802 2601 1967 1236 1642 1153 1078 ...
.. .. .. .. ..$ log10_total_features_endogenous : num [1:5586] 3.14 3.26 3.35 2.9 3.42 ...
.. .. .. .. ..$ total_counts_endogenous : num [1:5586] 3380 7332 10099 1833 12184 ...
.. .. .. .. ..$ log10_total_counts_endogenous : num [1:5586] 3.53 3.87 4 3.26 4.09 ...
.. .. .. .. ..$ pct_counts_endogenous : num [1:5586] 100 100 100 100 100 100 100 100 100 100 ...
.. .. .. .. ..$ pct_counts_top_50_features_endogenous : num [1:5586] 33.1 38.9 42.5 40.9 42.2 ...
.. .. .. .. ..$ pct_counts_top_100_features_endogenous: num [1:5586] 45 54.8 59.2 53.7 53.5 ...
.. .. .. .. ..$ pct_counts_top_200_features_endogenous: num [1:5586] 57.5 66.9 69 66.4 64.7 ...
.. .. .. .. ..$ pct_counts_top_500_features_endogenous: num [1:5586] 74.2 79.2 79.4 83.5 76.8 ...
.. .. .. .. ..$ total_features_feature_control : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_feature_control : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_features_MT : int [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_features_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ log10_total_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ pct_counts_MT : num [1:5586] 0 0 0 0 0 0 0 0 0 0 ...
.. .. .. .. ..$ is_cell_control : logi [1:5586] FALSE FALSE FALSE FALSE FALSE FALSE ...
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ assays :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field
.. .. ..$ data: NULL
.. .. ..and 14 methods.
.. ..@ NAMES : NULL
.. ..@ elementMetadata :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
.. .. .. ..@ rownames : NULL
.. .. .. ..@ nrows : int 33694
.. .. .. ..@ listData : Named list()
.. .. .. ..@ elementType : chr "ANY"
.. .. .. ..@ elementMetadata: NULL
.. .. .. ..@ metadata : list()
.. ..@ metadata :List of 1
.. .. ..$ name: chr "iMates-1"
Here is one of the four objects.
Could anyone of you help me.
Thank you
r s4
r s4
asked Nov 22 '18 at 15:25
user1826775user1826775
33
asked Nov 22 '18 at 15:25
user1826775user1826775
33
edited Nov 22 '18 at 22:49
user1826775
asked Nov 22 '18 at 15:25
user1826775user1826775
33
asked Nov 22 '18 at 15:25
user1826775user1826775
33
asked Nov 22 '18 at 15:25
user1826775user1826775
33
33
1
are you sure your sc_list contains anything? I'm not suremgetworks that way...
– iod
Nov 22 '18 at 15:32
It is not empty.
– user1826775
Nov 22 '18 at 15:57
Please put the additional information aboutstr(sc_list)from the comment in your question, i.e. edit your question: stackoverflow.com/posts/53434082/edit
– jogo
Nov 22 '18 at 18:44
@jogo edited the question. Please have a look.
– user1826775
Nov 22 '18 at 20:47
The objectsc_listis a list of S4-objects. The components of a S4-object are slots. The operator to access a slot is@(not$).
– jogo
Nov 22 '18 at 23:02
|
show 2 more comments
1
are you sure your sc_list contains anything? I'm not suremgetworks that way...
– iod
Nov 22 '18 at 15:32
It is not empty.
– user1826775
Nov 22 '18 at 15:57
Please put the additional information aboutstr(sc_list)from the comment in your question, i.e. edit your question: stackoverflow.com/posts/53434082/edit
– jogo
Nov 22 '18 at 18:44
@jogo edited the question. Please have a look.
– user1826775
Nov 22 '18 at 20:47
The objectsc_listis a list of S4-objects. The components of a S4-object are slots. The operator to access a slot is@(not$).
– jogo
Nov 22 '18 at 23:02
1
1
are you sure your sc_list contains anything? I'm not sure
mget works that way...– iod
Nov 22 '18 at 15:32
are you sure your sc_list contains anything? I'm not sure
mget works that way...– iod
Nov 22 '18 at 15:32
It is not empty.
– user1826775
Nov 22 '18 at 15:57
It is not empty.
– user1826775
Nov 22 '18 at 15:57
Please put the additional information about
str(sc_list) from the comment in your question, i.e. edit your question: stackoverflow.com/posts/53434082/edit– jogo
Nov 22 '18 at 18:44
Please put the additional information about
str(sc_list) from the comment in your question, i.e. edit your question: stackoverflow.com/posts/53434082/edit– jogo
Nov 22 '18 at 18:44
@jogo edited the question. Please have a look.
– user1826775
Nov 22 '18 at 20:47
@jogo edited the question. Please have a look.
– user1826775
Nov 22 '18 at 20:47
The object
sc_list is a list of S4-objects. The components of a S4-object are slots. The operator to access a slot is @ (not $).– jogo
Nov 22 '18 at 23:02
The object
sc_list is a list of S4-objects. The components of a S4-object are slots. The operator to access a slot is @ (not $).– jogo
Nov 22 '18 at 23:02
|
show 2 more comments
1 Answer
1
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I'm assuming sc_list is a list of lists, right?
If so, can you check if the following code works?
sc_list=mget(sc)
for (i in 1:5)
sc_list[[i]]$ue <- cF(sc_list[[i]], 2500, 1000, 5)
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
I got this error now. "$ operator is invalid for atomic vectors"
– user1826775
Nov 22 '18 at 15:38
1
can you post the output ofstr(sc_list)?
– feebarscevicius
Nov 22 '18 at 15:58
it is a very big output. But what I can see is that it starts with " List of 4". I hope this is what you were trying to confirm. The first line is like sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots .. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. ..@ rownames : NULL .. .. .. ..@ nrows : int 22496 .. .. .. ..@ listData :List of 2
– user1826775
Nov 22 '18 at 16:11
So it is a list of S4-objects.
– jogo
Nov 22 '18 at 16:27
@jogo: Yes, indeed. How should I fix this.
– user1826775
Nov 22 '18 at 17:51
|
show 1 more comment
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1 Answer
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oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
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active
oldest
votes
0
I'm assuming sc_list is a list of lists, right?
If so, can you check if the following code works?
sc_list=mget(sc)
for (i in 1:5)
sc_list[[i]]$ue <- cF(sc_list[[i]], 2500, 1000, 5)
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
I got this error now. "$ operator is invalid for atomic vectors"
– user1826775
Nov 22 '18 at 15:38
1
can you post the output ofstr(sc_list)?
– feebarscevicius
Nov 22 '18 at 15:58
it is a very big output. But what I can see is that it starts with " List of 4". I hope this is what you were trying to confirm. The first line is like sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots .. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. ..@ rownames : NULL .. .. .. ..@ nrows : int 22496 .. .. .. ..@ listData :List of 2
– user1826775
Nov 22 '18 at 16:11
So it is a list of S4-objects.
– jogo
Nov 22 '18 at 16:27
@jogo: Yes, indeed. How should I fix this.
– user1826775
Nov 22 '18 at 17:51
|
show 1 more comment
0
I'm assuming sc_list is a list of lists, right?
If so, can you check if the following code works?
sc_list=mget(sc)
for (i in 1:5)
sc_list[[i]]$ue <- cF(sc_list[[i]], 2500, 1000, 5)
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
I got this error now. "$ operator is invalid for atomic vectors"
– user1826775
Nov 22 '18 at 15:38
1
can you post the output ofstr(sc_list)?
– feebarscevicius
Nov 22 '18 at 15:58
it is a very big output. But what I can see is that it starts with " List of 4". I hope this is what you were trying to confirm. The first line is like sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots .. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. ..@ rownames : NULL .. .. .. ..@ nrows : int 22496 .. .. .. ..@ listData :List of 2
– user1826775
Nov 22 '18 at 16:11
So it is a list of S4-objects.
– jogo
Nov 22 '18 at 16:27
@jogo: Yes, indeed. How should I fix this.
– user1826775
Nov 22 '18 at 17:51
|
show 1 more comment
0
0
0
I'm assuming sc_list is a list of lists, right?
If so, can you check if the following code works?
sc_list=mget(sc)
for (i in 1:5)
sc_list[[i]]$ue <- cF(sc_list[[i]], 2500, 1000, 5)
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
I'm assuming sc_list is a list of lists, right?
If so, can you check if the following code works?
sc_list=mget(sc)
for (i in 1:5)
sc_list[[i]]$ue <- cF(sc_list[[i]], 2500, 1000, 5)
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
answered Nov 22 '18 at 15:34
feebarsceviciusfeebarscevicius
50426
50426
I got this error now. "$ operator is invalid for atomic vectors"
– user1826775
Nov 22 '18 at 15:38
1
can you post the output ofstr(sc_list)?
– feebarscevicius
Nov 22 '18 at 15:58
it is a very big output. But what I can see is that it starts with " List of 4". I hope this is what you were trying to confirm. The first line is like sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots .. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. ..@ rownames : NULL .. .. .. ..@ nrows : int 22496 .. .. .. ..@ listData :List of 2
– user1826775
Nov 22 '18 at 16:11
So it is a list of S4-objects.
– jogo
Nov 22 '18 at 16:27
@jogo: Yes, indeed. How should I fix this.
– user1826775
Nov 22 '18 at 17:51
|
show 1 more comment
I got this error now. "$ operator is invalid for atomic vectors"
– user1826775
Nov 22 '18 at 15:38
1
can you post the output ofstr(sc_list)?
– feebarscevicius
Nov 22 '18 at 15:58
it is a very big output. But what I can see is that it starts with " List of 4". I hope this is what you were trying to confirm. The first line is like sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots .. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. ..@ rownames : NULL .. .. .. ..@ nrows : int 22496 .. .. .. ..@ listData :List of 2
– user1826775
Nov 22 '18 at 16:11
So it is a list of S4-objects.
– jogo
Nov 22 '18 at 16:27
@jogo: Yes, indeed. How should I fix this.
– user1826775
Nov 22 '18 at 17:51
I got this error now. "$ operator is invalid for atomic vectors"
– user1826775
Nov 22 '18 at 15:38
I got this error now. "$ operator is invalid for atomic vectors"
– user1826775
Nov 22 '18 at 15:38
1
1
can you post the output of
str(sc_list)?– feebarscevicius
Nov 22 '18 at 15:58
can you post the output of
str(sc_list)?– feebarscevicius
Nov 22 '18 at 15:58
it is a very big output. But what I can see is that it starts with " List of 4". I hope this is what you were trying to confirm. The first line is like sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots .. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. ..@ rownames : NULL .. .. .. ..@ nrows : int 22496 .. .. .. ..@ listData :List of 2
– user1826775
Nov 22 '18 at 16:11
it is a very big output. But what I can see is that it starts with " List of 4". I hope this is what you were trying to confirm. The first line is like sc_1:Formal class 'SingleCellExperiment' [package "SingleCellExperiment"] with 10 slots .. ..@ int_elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots .. .. .. ..@ rownames : NULL .. .. .. ..@ nrows : int 22496 .. .. .. ..@ listData :List of 2
– user1826775
Nov 22 '18 at 16:11
So it is a list of S4-objects.
– jogo
Nov 22 '18 at 16:27
So it is a list of S4-objects.
– jogo
Nov 22 '18 at 16:27
@jogo: Yes, indeed. How should I fix this.
– user1826775
Nov 22 '18 at 17:51
@jogo: Yes, indeed. How should I fix this.
– user1826775
Nov 22 '18 at 17:51
|
show 1 more comment
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1
are you sure your sc_list contains anything? I'm not sure
mgetworks that way...– iod
Nov 22 '18 at 15:32
It is not empty.
– user1826775
Nov 22 '18 at 15:57
Please put the additional information about
str(sc_list)from the comment in your question, i.e. edit your question: stackoverflow.com/posts/53434082/edit– jogo
Nov 22 '18 at 18:44
@jogo edited the question. Please have a look.
– user1826775
Nov 22 '18 at 20:47
The object
sc_listis a list of S4-objects. The components of a S4-object are slots. The operator to access a slot is@(not$).– jogo
Nov 22 '18 at 23:02