computeZscores: Z score computation

Description Usage Arguments Value Examples

Description

Computes the z scores for every count in the matrix. The z score is defined in the log2 space as follows: zij = (lij - mujl)/ sigmajl, where l is the log2 transformed normalized count and mu and sigma the mean and standard deviation for gene j, respectively.

Usage

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computeZscores(ods, ...)

## S4 method for signature 'OutriderDataSet'
computeZscores(ods, peerResiduals = FALSE, ...)

Arguments

ods

OutriderDataSet

...

Further arguments passed on to ZscoreMatrix.

peerResiduals

If TRUE, PEER residuals are used to compute Z scores

Value

An OutriderDataSet containing the Z score matrix "zScore" and the log2 fold changes "l2fc" as asasys.

Examples

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ods <- makeExampleOutriderDataSet()
ods <- estimateSizeFactors(ods)

ods <- controlForConfounders(ods, implementation="pca")
ods <- computeZscores(ods)

zScore(ods)[1:10,1:10]
assay(ods, "l2fc")[1:10,1:10]

gagneurlab/OUTRIDER documentation built on Oct. 24, 2020, 6:49 p.m.