computeZscores {OUTRIDER} | R Documentation |
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.
computeZscores(ods, ...) ## S4 method for signature 'OutriderDataSet' computeZscores(ods, peerResiduals = FALSE, ...)
ods |
OutriderDataSet |
... |
Further arguments passed on to |
peerResiduals |
If TRUE, PEER residuals are used to compute Z scores |
An OutriderDataSet containing the Z score matrix "zScore" and the log2 fold changes "l2fc" as asasys.
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]