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Old 11-18-2014, 01:41 PM   #1
sylvian
Junior Member
 
Location: Penn

Join Date: Jun 2013
Posts: 4
Default easyRNAseq problem: Error in aggregate.data.frame

easyRNAseq terminates with the error:

Error in aggregate.data.frame(as.data.frame(x), ...) :
no rows to aggregate


I use easyRNAseq to enter my data for DESeq:

> library(easyRNASeq)
> library(BSgenome.Hsapiens.UCSC.hg19)
> setwd('/home/sylvian/SerumFedStarved/DESeq/')
> chr.sizes=seqlengths(Hsapiens)
> bamfiles=dir(getwd(), pattern='*.bam$')
> conditions=c('fed','starved','fed','starved','fed','starved')
> names(conditions)<-c('DRSNpilot1_STARhg19_paired_sorted.bam','DRSNpilot2_STARhg19_paired_sorted.bam','TQ24_STARhg19_paired_sorted.bam','TQ25_STARhg19_paired_sorted.bam','TQ28_STARhg19_paired_sorted.bam','TQ29_STARhg19_paired_sorted.bam')
> rnaseqgenes<-easyRNASeq(filesDirectory=getwd(),
+ organism='Hsapiens',
+ chr.sizes=chr.sizes,
+ readLength=100L,
+ annotationMethod='biomaRt',
+ format='bam',
+ count='genes',
+ summarization='geneModels',
+ filenames=bamfiles,
+ conditions=conditions,
+ normalization=TRUE,
+ fitType='local',
+ outputFormat='DESeq')
Checking arguments...
Fetching annotations...
Computing gene models...
Summarizing counts...
Processing DRSNpilot1_STARhg19_paired_sorted.bam
Error in aggregate.data.frame(as.data.frame(x), ...) :
no rows to aggregate

Has anybody by any chance had the same problem and knows how to fix this?

I used to do
chr.sizes=as.list(seqlengths(Hsapiens)
but this now produces an error:
Error in easyRNASeq(filesDirectory = getwd(), organism = "Hsapiens", chr.sizes = chr.sizes, :
chr.sizes should be a named list of integers. 'Use 'as.integer' to convert from numeric.


chr.sizes=seqlengths(Hsapiens) produces

chr1 chr2 chr3
249250621 243199373 198022430
chr4 chr5 chr6
191154276 180915260 171115067
chr7 chr8 chr9
159138663 146364022 141213431
...

Thanks a lot
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