log_transform: Log transformation

In szymczak-lab/QCnormSE: Quality Control of Normalized Gene Expression Data

Log transformation

Description

Performs log transformation of expression values (log2). Values below zero will be set to zero and if zero values are available a pseudocount will be added.

Usage

log_transform(se, assay = 1, pseudocount = 1)

Arguments

se	RangedSummarizedExperiment-class object
assay	Character or integer. Name or number of assay containing expression data to be log transformed.
pseudocount	Numeric. Value added to expression values before log transformation (relevant for count data containing zero values).

Value

RangedSummarizedExperiment-class object with normalized log transformed expression values in additional assay called <assay>.log.

Examples

data("se.probeset")

se.probeset = log_transform(se = se.probeset)

szymczak-lab/QCnormSE documentation built on March 25, 2023, 1:05 p.m.