tgambin
commented
7 years ago Assuming that you have already defined the following objects: bedFile, bamFiles, sampleNames, outputDir Could you please, try to run the following lines one by one and see if/when you get error?:
`
library(Rsubread)
library(data.table)
library(parallel)
bed <- fread(bedFile)
df <- data.frame(cbind(1:nrow(bed), bed))
colnames(df) <- c("GeneID", "Chr", "Start", "End", "Strand")
if (!file.exists(outputDir)){dir.create(outputDir)}
i <- 1
file <- bamFiles[i]
prefix <- sampleNames[i]
outputFile <- paste0(outputDir, prefix, "_rpkm2.txt")
res <- featureCounts(files=file, annot.ext=df, allowMultiOverlap=TRUE, nthreads=3)
total <- sum(res$stat[2])
counts <- data.frame(res$counts)
colnames(counts) <- "count"
counts$RPKM <- as.numeric(1e9 * as.numeric(counts$count)) / as.numeric(as.numeric(df$End - df$Start) * as.numeric(total))
write.table(counts, file=outputFile, sep="\t", col.names=T, row.names=F, quote=F)`
NJ2012
Rt-2017
Hoxus
vmrosario
Dear sir, madam, I keep running into the following problem. It is not to me clear what this means and how to resolve. I hope you can help me further.
command: calcRPKMsFromBAMs(bedFile,bamFiles , sampleNames, rpkmDir,4)
In fread(bedFile) : Bumped column 1 to type character on data row 213577, field contains 'X'. Coercing previously read values in this column from logical, integer or numeric back to character which may not be lossless; e.g., if '00' and '000' occurred before they will now be just '0', and there may be inconsistencies with treatment of ',,' and ',NA,' too (if they occurred in this column before the bump). If this matters please rerun and set 'colClasses' to 'character' for this column. Please note that column type detection uses the first 5 rows, the middle 5 rows and the last 5 rows, so hopefully this message should be very rare. If reporting to datatable-help, please rerun and include the output from verbose=TRUE. 2: In mclapply(1:length(bamFiles), function(i) { : all scheduled cores encountered errors in user code