rnaNormalize {ORFik} | R Documentation

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

### 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.

[Package ORFik version 1.8.6 Index]