isoNorm: Normalize count matrix

In lpantano/isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Normalize count matrix

Description

This function normalizes raw count matrix using DESeq2::rlog() function from DESeq2::DESeq2-package.

Usage

isoNorm(ids, formula = NULL, maxSamples = 50)

Arguments

ids	Object of class IsomirDataSeq.
formula	Formula that will be used for normalization.
maxSamples	Maximum number of samples to use with DESeq2::rlog(), if not limma::voom() is used.

Value

IsomirDataSeq object with the normalized count matrix in a slot. The normalized matrix can be access with counts(ids, norm=TRUE).

Examples

data(mirData)
ids <- isoCounts(mirData, minc=10, mins=6)
ids <- isoNorm(mirData, formula=~condition)
head(counts(ids, norm=TRUE))

lpantano/isomiRs documentation built on Aug. 26, 2024, 3:34 a.m.