M3D_calc_var: Calculate Gene Variables

In M3Drop: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Description

Calculates a suite of gene-specific variables including: mean, dropout rate, and their standard errors.

Usage

	bg__calc_variables(expr_mat)

Arguments

expr_mat

a numeric matrix of normalized (not log-transformed) expression values, columns = samples, rows = genes.

Details

Calculates mean expression and its standard error ( sd/sqrt(n) ), and the dropout rate, proportion of observations that are zero, and its standard error ( sqrt(p*(1-p)/n) ) for each gene in the dataset. Performs various checks to ensure expression matrix is of suitable format for M3Drop. Removes undetected genes if they are present.

Value

Named list of calculated values: s = vector of mean expression for each gene s_stderr = vector of mean expression standard error for each gene p = vector of dropout rate for each gene p_stderr = vector of dropout rate standard error for each gene

M3Drop documentation built on Nov. 8, 2020, 5:06 p.m.