counts_to_rle: Size Factor normalization as used by DESeq for differential...

Description Usage Arguments Value

Description

First the geometric mean of each gene across all cells is calculated. The size factor for each cell is the median across genes of the ratio of the expression to the gene’s geometric mean. Spike-ins should be excluded from the calculation of total expression in order to correct for total cell RNA content, therefore they should be specified to exclude them from downstream analysis

Usage

1
counts_to_rle(expr_mat, spikes = NULL)

Arguments

expr_mat

Input matrix with expression values for genes in the form (Genes x Samples)

spikes

A vector of genes that were spike-ins in the original experiment

Value

A matrix with SF normalized RLE values


ssarda/genomeutils documentation built on May 30, 2019, 8:42 a.m.