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.

You simply run featureCounts() with countMultiMappingReads=TRUE and fraction=TRUE.

The help page for featureCounts() says

"fraction:

logical indicating if fractional counts will be produced for multi-mapping reads. If TRUE, a fractional count, 1/n, will be generated for each reported alignment of a multi-mapping read, where n is the total number of alignments reported for that read. countMultiMappingReads must be set to TRUE when fraction is TRUE."

Both edgeR and limma accept fractional counts for analyzing RNA-seq data.

If you must round the counts, then rounding to the nearest integer (up or down) would be far better than rounding up. You can easily do this by:

fc <- featureCounts(files,countMultiMappingReads=TRUE,fraction=TRUE)
fc$counts[] <- round(fc$counts)

Note: fractional counting was introduced in Rsubread 1.20.0, so you must be using the latest release of R and Bioconductor.