DEgenes: Differentially Expressed Genes Between Two Groups

In jlaffy/statistrics: Basic Statistics For Single-Cell (or bulk) RNA Analyses

Description

Differentially Expressed Genes Between Two Groups

Usage

DEgenes(k, mat, fc.value = 3, p.value = 10^(-4), fc.sort = T,
  pval.sort = F, adjust.method = NULL, returning = "pval", ...)

Arguments

k	a list of character vectors; sets of cell members belonging to each cluster.
mat	matrix of vars. vs. obs. matrix is split into two: i) vars that are in k; ii) vars not in k.
fc.value	fold change value below which differential gene expression is deemed insignificant.
p.value	p-value above which differential gene expression is deemed insignificant.
fc.sort	if TRUE, significantly differentially expressed genes are sorted by fold change (highest first). Default is TRUE.
pval.sort	if TRUE, significantly differentially expressed genes are sorted by p.value (highest first). pval.sort=TRUE overrides fc.sort=TRUE. Default is FALSE.
adjust.method	NULL or character string. If NULL, do not adjust p-values. If string, adjust p-values using the method specified.
returning	return one of p-values, fold changes, or both from the output of sig() call.
...	other args to be passed to p_val or fold_change through call to sig.

Value

numeric vector of p-values named with gene names.

jlaffy/statistrics documentation built on May 23, 2019, 4:04 a.m.