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  • 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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