Implement DESeq2 like normalization

[lpantano]

Add the code that from a count matrix, can get the size factor to normalize the data.

So, input would be: count data and output: normalized count data.

In R the code is like this:

loggeomeans <- rowMeans(log(counts))
sf <- apply(counts, 2, function(cnts) {
      exp(median((log(cnts) - loggeomeans)[is.finite(loggeomeans) & cnts > 0]))
    })
sf <- sf/exp(mean(log(sf)))
t(t(counts)/sf)

This code can be inside libs/math.py

[shruthibandyadka]

Is this count matrix the one created in gff/convert.py ? (example file at data/examples/gff/gff_tsv_expression_counts.tsv)

[lpantano]

Hi!
This would be to do an extra step from that matrix. So, the idea is once you have the matrix, apply this calculation to get a normalize one.