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tg369 ▴ 10
@tg369-9320
Last seen 2.9 years ago
United Kingdom

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.

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

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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.

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Your software is two Bioconductor releases out of date, which is why it doesn't have the latest features.

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

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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)

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@gordon-smyth
Last seen 9 minutes ago
WEHI, Melbourne, Australia

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$counts[] <- round(fc$counts)

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

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Is this option available for the command line version of FeatureCounts as well?

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Yes, it is called '--fraction'.