Hello everybody,
I am using the library rapidr of bioconductor, I am running it without problems as follows
library("RAPIDR")
makeBinnedCountsFile("SRR611842_2.bam","SRR611842_2","binnecounts.r",mask=NULL,k=20000)
> SampleID=c("SRR611842_2")
> DX=c("T21")
> Gender=c("Male")
> frame= data.frame(SampleID, DX, Gender)
No problems until here, but when i do
> createReferenceSetFromCounts("binnecounts.r",frame)
Loading binned counts file
Checking every sampleID has an outcome
here i have the following error
Error in `*tmp*`[[jj]] : subscript out of bounds
Suggestions?
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.3 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=hr_HR.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=hr_HR.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=hr_HR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=hr_HR.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.4.0 BSgenome_1.36.3
[3] rtracklayer_1.28.10 Biostrings_2.36.4
[5] XVector_0.8.0 GenomicRanges_1.20.6
[7] GenomeInfoDb_1.4.3 IRanges_2.2.7
[9] S4Vectors_0.6.6 BiocGenerics_0.14.0
[11] RAPIDR_0.1.1
loaded via a namespace (and not attached):
[1] XML_3.98-1.3 Rsamtools_1.20.4 bitops_1.0-6
[4] GenomicAlignments_1.4.1 chron_2.3-47 futile.options_1.0.0
[7] zlibbioc_1.14.0 data.table_1.9.6 futile.logger_1.4.1
[10] BiocParallel_1.2.21 lambda.r_1.1.7 tools_3.2.2
[13] PropCIs_0.2-5 RCurl_1.95-4.7
>
