How to modify function of samr.estimate.depth of samr
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yuan.qing ▴ 10
@yuanqing-8002
Last seen 9.3 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 • 962 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 14 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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