contrast_the_group_to_the_rest {celaref} | R Documentation

## contrast_the_group_to_the_rest

### Description

Internal function to calculate differential expression within an experiment between a specified group and cells not in that group.

### Usage

    contrast_the_group_to_the_rest(dataset_se, the_group,
      pvalue_threshold = 0.01, n.group = Inf, n.other = n.group * 5)

### Arguments

`dataset_se` | Datast summarisedExperiment object.
`the_group` | group to test
`pvalue_threshold` | Default = 0.01
`n.group` | How many cells to keep for each group in groupwise comparisons. Default = Inf
`n.other` | How many cells to keep from everything not in the group. Default = n.group * 5

### Details

This function should only be called by `contrast_each_group_to_the_rest` (which can be passed a single group name if desired). Else 'pofgenes' will not be defined.

MAST is supplied with log2(counts + 1.1), and zlm called with model '~ TvsR + pofgenes' . The p-values reported are from the hurdle model. FDR is with default fdr/BH method.

### Value

A tibble, the within-experiment de_table (differential expression table), for the group specified.

### See Also

`contrast_each_group_to_the_rest`

[Package celaref version 1.6.0 Index]