matLog2: log2-scale transform a dense OR sparse matrix

In YosefLab/VISION: Functional interpretation of single cell RNA-seq latent manifolds

log2-scale transform a dense OR sparse matrix

Description

This avoids the creation of a dense intermediate matrix when operating on sparse matrices

Usage

matLog2(spmat, scale = FALSE, scaleFactor = 1e+06)

Arguments

spmat	sparse Matrix
scale	boolean - whether or not to scale the columns to sum to 'scale_factor'
scaleFactor	if scale = TRUE, columns are scaled to sum to this number

Details

Either performs result <- log2(spmat+1) or if scale = TRUE returns result <- log2(spmat/colSums(spmat)*scaleFactor + 1)

Value

logmat sparse Matrix

YosefLab/VISION documentation built on June 14, 2024, 5:27 p.m.