writeCompleteResults : Error in data.frame(..., check.names = FALSE)

[YanliangDou]

Hi ,

When I run

writeCompleteResults(jscs, outfile.prefix="./output_R/")

there is one error

Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 491717, 0

My whole script like below:

`BiocManager::install("JunctionSeq")

library(JunctionSeq)
library(JctSeqData)

######################
decoder <- read.table("decoder.bySample.txt",header=TRUE,stringsAsFactors=FALSE);
design <- data.frame(condition = factor(decoder$group.ID));
geneID.to.symbol.file <- read.table("ensid.2.symbol.txt",header=TRUE,stringsAsFactors=FALSE);
gff.file <- c("output_final/withNovel.forJunctionSeq.gff.gz");
#The count files:
countFiles <- paste0("./output_final/",decoder$sample.ID,"/QC.spliceJunctionAndExonCounts.withNovel.forJunctionSeq.txt.gz");
#######################################################################################
jscs = readJunctionSeqCounts(countfiles = countFiles,
samplenames = decoder$sample.ID,
design = design,
flat.gff.file = gff.file,
gene.names = geneID.to.symbol.file,
nCores = 1,
verbose=TRUE,
analysis.type = "junctionsAndExons"
);
######################################################################################
#replace the estimation function with a version that takes an external size factor.

I Should have added this long ago...

estimateJunctionSeqSizeFactors.forced <- function( jscs , sizeFactors, verbose = FALSE){
stopifnot( is( jscs, "JunctionSeqCountSet") )
sizeFactors(jscs) <- sizeFactors
sizeFactors(jscs@DESeqDataSet) <- rep(sizeFactors(jscs),2)
fData(jscs)$baseMean <- rowMeans(counts(jscs, normalized= T))
fData(jscs)$baseVar <- rowVars(counts(jscs, normalized=T))
jscs@altSizeFactors <- data.frame()
return(jscs);
}

#Calculate size factors using your favorite method.
#I recommend the upper quartile method, shown below:
SF <- sapply(1:ncol(jscs@geneCountData),function(i){
quantile(jscs@geneCountData[,i],p=0.75);
})
#Now copy in those size factors:
jscs <- estimateJunctionSeqSizeFactors.forced(jscs,sizeFactors=SF)
###########################################################################

writeSizeFactors(jscs, file = "sizeFactors.txt");
writeCompleteResults(jscs, outfile.prefix="./output_R/")`