normalize_counts: Calculate normalized counts.
In vari-bbc/bbcRNA: Bulk RNA-seq workflow for VAI BBC

Description Usage Arguments Details Value Methods (by class) See Also

Calculate normalized counts.

normalize_counts(x, ...)

## S4 method for signature 'BbcSE'
normalize_counts(x, de_pkg = "edger")

## S4 method for signature 'DGEList'
normalize_counts(x)

`x`	A BbcSE object or a DGEList or a DESeqDataSet.
`...`	Not used currently
`de_pkg`	"edger" or "deseq2". Only used if x is a BbcSE

Normalization uses methods from the package corresponding to the de_pkg paramter:

edger: Uses edgeR::cpm with normalized.lib.sizes = TRUE and log = TRUE
deseq2: Not implemented yet.

A BbcSE object or a matrix or....

BbcSE: For de_pkg="edger", a SummarizedExperiment object is created and stored in the BbcEdgeR object in the edger slot. Group average log normalized counts are also calculated and stored as rowData.
DGEList: log normalized counts returned as a matrix.

cpm

vari-bbc/bbcRNA documentation built on Nov. 10, 2020, 11:09 p.m.