contrast_the_group_to_the_rest: contrast_the_group_to_the_rest

In MonashBioinformaticsPlatform/celaref: Single-cell RNAseq cell cluster labelling by reference

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,
  factors_to_rm = c())

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
factors_to_rm	If there are extra confounding factors that should be removed from MAST's zlm model (e.g individual, run), specify the column name(s) from colData in a vector here. Default=c().

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

MonashBioinformaticsPlatform/celaref documentation built on June 5, 2019, 11:35 a.m.