M3D_calc_var: Calculate Gene Variables
In tallulandrews/M3D: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Description Usage Arguments Details Value

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

1	bg__calc_variables(expr_mat)

expr_mat

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

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.

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

tallulandrews/M3D documentation built on May 31, 2019, 2:55 a.m.