problem with in rapidr createReferenceSetFromCountss
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Entering edit mode
@pau-marc-munoz-torres-6731
Last seen 4.9 years ago
Barcelona

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         

 

rapidr createReferenceSetFromCounts • 754 views
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0
Entering edit mode
@pau-marc-munoz-torres-6731
Last seen 4.9 years ago
Barcelona

Problem solved, DX must be Dx

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