rnaNormalize: Normalize a data.table of coverage by RNA seq per position

In ORFik: Open Reading Frames in Genomics

Description

Normalizes per position per gene by this function: (reads at position / min(librarysize, 1) * number of genes) / fpkm of that gene's RNA-seq

Usage

rnaNormalize(coverage, df, dfr = NULL, tx, normalizeMode = "position")

Arguments

coverage	a data.table containing at least columns (count/score, position), it is possible to have additionals: (genes, fraction, feature)
df	an ORFik experiment
dfr	an ORFik experiment of RNA-seq to normalize against. Will add RNA normalized to plot name if this is done.
tx	a GRangesList of mrna transcripts
normalizeMode	a character (default: "position"), how to normalize library against rna library. Either on "position", normalize by number of genes, sum of reads and RNA seq, on tx "region" or "feature": same as position but RNA is split into the feature groups to normalize. Useful if you have a list of targets and background genes.

Details

Good way to compare libraries

Value

a data.table of normalized transcripts by RNA.

ORFik documentation built on March 27, 2021, 6 p.m.