I was using featureCounts function from the R package ("Rsubread"). I need to count reads which are mapped to multiple regions but want to represent that as 1/n (where n= number of alignments). However I am unable to find the argument 'fraction' in the R function featureCounts.

DEseq2 doesn't take fraction values, do you suggest to round up those values? if yes then can we implement that in featureCounts.

Thank you for your advice on the above points.

Your R and/or Rsubread are probably old? Update them to the latest version and you should be able to see the 'fraction' argument.

I am using Rsubread_1.16.1 and updated all.

My R version is:

R version 3.1.2 (2014-10-31)

Platform: x86_64-unknown-linux-gnu (64-bit)

Still it is not working.

The current version of R is 3.2.2 and the current version of Rsubread is 1.20.2.

Your software is two Bioconductor releases out of date, which is why it doesn't have the latest features.

You need to update to the latest versions of R and Bioconductor, as Wei already advised you.

Many thanks Gordon and Wei, that is working now after updating R version.

Thank you very much Gordon.

However, I wonder why I am getting this error message:

Error in featureCounts(file = "co2a_STAR_gencodeAligned.out.sam", :

unused argument (fraction = TRUE)

Please could you advice me.