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)

Arguments

dataset_se

Datast summarisedExperiment object.

the_group

group to test

pvalue_threshold

Default = 0.01

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 1.0.1 Index]