mgkit.counts.scaling module¶
Scaling functions for counts
-
mgkit.counts.scaling.
scale_deseq
(dataframe)¶ New in version 0.1.13.
Scale a dataframe using the deseq scaling. Uses
scale_factor_deseq()
-
mgkit.counts.scaling.
scale_factor_deseq
(dataframe)¶ New in version 0.1.13.
Returns the scale factor according to he deseq paper. The columns of the dataframe are the samples.
size factor \(\hat{s}_{j}\) for sample j (from DESeq paper).
\[\hat{s}_{j} = median_{i} ( \frac {k_{ij}} { \left ( \prod_{v=1}^{m} k_{iv} \right )^{1/m} } )\]
-
mgkit.counts.scaling.
scale_rpkm
(dataframe, gene_len)¶ New in version 0.1.14.
Perform an RPKM scaling of the pandas dataframe/series supplied using the gene_len series containing the gene sizes for all elements of dataframe
\[RPKM =\frac {10^{9} \cdot C} {N \cdot L}\]