normalize_data — normalize_data • metamoRph

Applies sample level normalization and high variable feature (gene) selection. If cpm scaling selected, then scuttle::calculateCPM is applied before log1p (if TRUE). zscale will apply log1p first (if TRUE).

Usage

normalize_data(feature_by_sample, sample_scale = "cpm", log1p = TRUE)

Arguments

feature_by_sample: features (row) by sample (column) matrix
sample_scale: Options include cpm, seurat, zscale, and none
log1p: Default is TRUE

Value

a list object containing the prcomp "center" and "scale" values for use in the metamoRph function

Details

This function is used by both metamoRph::metamoRph and metamoRph::run_pca