computeZscores: Z score computation

In OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Description

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

Usage

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

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]

OUTRIDER documentation built on Nov. 8, 2020, 5:16 p.m.