getDiggitEmpiricalQvalues {MOMA} | R Documentation

## Compute the empirical q-values of each genomic-event/VIPER gene pair

### Description

Use against the background distribution of associations with a given set of 'null' VIPER genes (i.e. low activity TFs)

### Usage

    getDiggitEmpiricalQvalues(vipermat, nes, null.TFs, alternative = "both")

### Arguments

`vipermat` | viper inferences matrix, samples are columns, rows are TF entrez gene IDs
`nes` | scores for each mutation (rows) against each TF (columns)
`null.TFs` | low-importance TFs used to calculate null distributions
`alternative` | Alternative defaults to 'both' : significant p-values can come from both sides of the null distribution

### Value

A named list of qvalues for each TF/cMR protein. Each entry contains a vector of q-values for all associated events; names are gene ids

[Package MOMA version 1.2.0 Index]