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Error in colnames<- #21
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This could be a cache issue. You should clear your cache. gbm <- curatedTCGAData::curatedTCGAData("GBM", "CNVSNP", FALSE)
#> snapshotDate(): 2019-01-15
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> downloading 0 resources
#> loading from cache
#> '/home/mr148//.ExperimentHub/670'
#> Loading required package: RaggedExperiment
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> downloading 0 resources
#> loading from cache
#> '/home/mr148//.ExperimentHub/671'
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> downloading 0 resources
#> loading from cache
#> '/home/mr148//.ExperimentHub/674'
#> see ?curatedTCGAData and browseVignettes('curatedTCGAData') for documentation
#> downloading 0 resources
#> loading from cache
#> '/home/mr148//.ExperimentHub/685'
#> harmonizing input:
#> removing 6776 sampleMap rows not in names(experiments)
#> removing 7 colData rownames not in sampleMap 'primary'
gbm.ra <- gbm[[1]]
gbm.ra
#> class: RaggedExperiment
#> dim: 146852 1104
#> assays(2): Num_Probes Segment_Mean
#> rownames: NULL
#> colnames(1104): TCGA-02-0001-01C-01D-0182-01
#> TCGA-02-0001-10A-01D-0182-01 ... TCGA-RR-A6KC-01A-31D-A33S-01
#> TCGA-RR-A6KC-10A-01D-A33V-01
#> colData names(0): Created on 2019-01-23 by the reprex package (v0.2.1) |
You're right. Thanks! |
More on that, this is actually how I run into this error:
|
Ah yes, this looks like an index issue after subsetting. |
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I'm pulling a
RaggedExperiment
from TCGA:Looks like there is a small bug in the
colnames<-
replacement method:The text was updated successfully, but these errors were encountered: