normalizeTCWithFeatures: Normalize Total Count with Features

In khodosevichlab/CellAnnotatoR: Automated marker-based cell type annotation

Normalize Total Count with Features

Description

Normalize 'cm' matrix using total counts and then column-wise min-max scaling

Usage

normalizeTCWithFeatures(
  cm,
  max.quantile = 0.95,
  max.smooth = 1e-10,
  transpose = T
)

Arguments

cm	gene count matrix with cells by columns and genes by rows. May be in raw, TC-normalized or tf-idf-normalized format (in case of tf-idf, 'prenormalized' must be set to 'T')
max.quantile	quantile to be used for max estimation during scaling

Value

Normalized matrix of the same shape as 'cm'

khodosevichlab/CellAnnotatoR documentation built on June 29, 2022, 9:12 p.m.