tmm: Trimmed Mean of M-Values (TMM) Normalization

Description Usage Arguments Value Author(s) See Also Examples

Description

TMM normalization is recommended for RNA-seq data generally when the majority of genes are not differentially expressed. We use this as a quality control tool when plotting counts per gene.

Usage

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tmm(object)

## S4 method for signature 'bcbioRNASeq'
tmm(object)

## S4 method for signature 'DESeqDataSet'
tmm(object)

## S4 method for signature 'matrix'
tmm(object)

Arguments

object

Object.

Value

matrix.

Author(s)

Michael Steinbaugh

See Also

Other Data Functions: counts, metrics, tpm

Examples

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# bcbioRNASeq ====
tmm(bcb_small) %>% summary()

# DESeqDataSet ====
tmm(dds_small) %>% summary()

# matrix ====
counts(bcb_small) %>% tmm() %>% summary()

roryk/bcbioRnaseq documentation built on May 27, 2019, 10:44 p.m.