easyRNASeq Unused Arguments

Question

[tessahu888]

Hi,

I ran the Tophat2 mapping for RNA-Seq using reference genome hg38. Now I'm trying to generate a count table using my accepted_hits.bam files using the R package easyRNASeq.

I'm getting an error in R:

Error in simpleRNASeq(filesDirectory=getwd( ), format="bam", organism="Hsapiens", :
    unused arguments(filesDirectory=getwd( ), format="bam", organism="Hsapiens", readLength="100L,        
    fileNames=c("accepted_control_hits.bam", "accepted_250_hits.bam"),
    annotationMethod="gtf", annotationFile="UCSC_genes_hg38.gtf", count="genes",
    outputFormat="edgeR", conditions=conditions, summarization="geneModels")

where the code is:

count.table<-simpleRNASeq(filesDirectory=getwd( ), format="bam", organism="Hsapiens", :
    unused arguments(filesDirectory=getwd( ), format="bam", organism="Hsapiens", readLength="100L,
    fileNames=****c("accepted_control_hits.bam", "accepted_250_hits.bam"),
    annotationMethod="gtf", annotationFile="UCSC_genes_hg38.gtf", count="genes",
    outputFormat="edgeR", conditions=conditions, summarization="geneModels")

Any ideas would be appreciated!

tessaca

[Michael]

After further testing, I should add that there is seemingly a lot of problems with this package now, and trying to circumvent those it should be effectively called difficultRNASeq, so I am considering to use something else.

[tessahu888]

Yes, it seems very problematic. Going to try your suggestion with the new function name simpleRNAseq. Thanks! I am thinking that I also might start a bedtools multicov trial.

Answer 1

[Michael]

You are using the function simpleRNASeq with the arguments of the function easyRNASeq.

easyRNASeq was depricated in favor of simpleRNASeq, but the tutorial was not updated. You have to use the reference manual to find out the right usage, there are some changes, for the lacking documentation using these functions neither seems very easy nor simple to me, I have just figured out how to use the new interface :)

Another change is that seemingly simpleRNASeq doesn't have an option to make an edgeR or DESeq object directly any more. Further it doesn't seem to recognize that BAMs are sorted by older versions of samtools. I have to still figure that out.

Here is some example code for a call:

library(easyRNASeq)
anns = "/pathto/mygenome.gff3"
args <- c('test.fastq.gz.sorted.bam')
annotParam <- AnnotParam(datasource=anns, type="gff3")
bamParam <- BamParam(paired = FALSE, stranded = TRUE, yieldSize = 1000000L)
param <- RnaSeqParam(annotParam = annotParam, bamParam = bamParam, countBy = c("transcripts"), precision = "bp")
simpleRNASeq(bamFiles = getBamFileList(args), param = param, nnodes = 8, verbose = TRUE, override = TRUE)