How to modify function of samr.estimate.depth of samr
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yuan.qing • 0
@yuanqing-8002
Last seen 7.4 years ago
United States

How to modify the source code in samr? I want to do the TMM normalization.

I had the following:

SAMseq.test = SAMseq(countdata1, finaldata1$Group, geneid=as.character(rownames(countdata1)), 
                    genenames=as.character(rownames(countdata1)),
                    resp.type="Two class unpaired",nperms=1000, random.seed = 1234, fdr.output=0.2)
print(SAMseq.test)


In case of TMM normalization, one can manipulate the function, but how?
"samr.estimate.depth" of the source code as below and then resintall the package with the new source file.
# samr.estimate.depth
# function (x) 
# {
#   library(edgeR)
#   cmeans <- calcNormFactors(x) * colSums(x)
#   depth <- cmeans/mean(cmeans)
#   return(depth)
# }
# <environment: namespace:samr>

If anyone knows how?

Thanks a lot!

samr • 621 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 3 hours ago
United States

The samr package isn't part of Bioconductor, so this isn't the appropriate forum. In addition, this forum is not really about how to program using R.

I just did a google search for 'R package modify' and came up with lots of apparently useful hits. You might try the same.
 

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