bg__calc_variables {M3Drop} | R Documentation

## Calculate Gene Variables

### 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

[Package M3Drop version 1.14.0 Index]