computeZscores: Z score computation

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

Z score computation

Description

Computes the z scores for every count in the matrix. The z score is defined in the log_2 space as follows: z_{ij} = \frac{l_{ij} - \mu_j^l}{ \sigma_j^l} where l is the log_2 transformed normalized count and \mu and \sigma the mean and standard deviation for gene j and sample i, 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]

gagneurlab/OUTRIDER documentation built on April 29, 2024, 2:22 a.m.