Fraction arguments for multi mapping reads in featureCounts in Rsubread
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tg369 ▴ 10
@tg369-9320
Last seen 18 months 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.

Thank you for your advice on the above points.

rsubread • 2.9k views
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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Your software is two Bioconductor releases out of date, which is why it doesn't have the latest features.

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

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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)

Please could you advice me.

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@gordon-smyth
Last seen 4 hours 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 <- 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.

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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'.

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