divide_seq: Express a data frame of counts as reads per pattern per...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Express a data frame of counts as reads per pattern per million.

Description

This uses a sequence pattern rather than length to normalize sequence. It is essentially fancy pants rpkm.

Usage

divide_seq(counts, ...)

Arguments

counts	Read count matrix.
...	Options I might pass from other functions are dropped into arglist.

Value

The RPseqM counts

See Also

[edgeR] [Rsamtools::FaFile()] [Biostrings::PDict()] [Biostrings::vcountPDict()] [GenomeInfoDb] [GenomicRanges]

Examples

## Not run: 
 cptam <- divide_seq(cont_table, fasta = "mgas_5005.fasta.xz", gff = "mgas_5005.gff.xz")

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.