bg__nbumiGroupDE {M3Drop} | R Documentation

## Perform Traditional Differential Expression

### Description

Performs traditional (i.e. compare defined groups) differential expression using a negative binomial model with MM zero-inflation. Functions tagged with "bg__" are not meant for direct usage and are not available in the Bioconductor release.

### Arguments

`counts` | a numeric matrix of raw UMI counts, columns = samples, rows = genes.
`fit` | fit NB UMI model from NBumiFitModel
`groups` | a vector of biological group IDs for each cell(columns).

### Details

THIS FUNCTION SHOULD NOT BE USED.

`unfinished__nbumiGroupDE` Uses a log-likelihood ratio test to perform model selection between a model of constant mean expression vs a model of different mean expression across the biological groups. Probabilities of observing the data given the model are calculated using a negative binomial distribution with means adjusted for the total molecules detected per cell and dispersion fit to observed variance and adjusted to the mean of each group based on a globally fit power-law relationship. Significance is evaluated using the chi-square distribution.

### Value

A table of fold mean expression differences for each biological group relative to the global mean expression level with raw p-values and FDR corrected p-values for each gene.

### Examples

    #library(M3DExampleData)
    #counts <- as.matrix(Mmus_example_list$data);
    #counts <- counts[rowSums(counts) > 0,];
    #counts <- counts[1:1000,]
    #fit <- NBumiFitModel(counts);
    #DE_output <- bg__nbumiGroupDE(counts, fit, Mmus_example_list$labels)

[Package M3Drop version 1.12.0 Index]