findSignatures: Identify gene signatures.

In edroaldo/fusca: Framework for Unified Single-Cell Analysis

Identify gene signatures.

Description

Identify gene signatures using the wilcoxon test or template-matching methods.

Usage

findSignatures(
  object,
  assay.type = "RNA",
  column = "population",
  test.use = "wilcox",
  pos.only = TRUE,
  min.pct = 0.1,
  fc.threshold = 0.25,
  fc.tm = FALSE
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
column	character; specify the groups to compare.
test.use	character; differential expression test to use. Alternative is based on template-matching. Possible values: wilcox or template.
pos.only	logical; use only upregulated genes.
min.pct	numeric; minimum percentage.
fc.threshold	numerical; fold change threshold.
fc.tm	logical; whether to include fold change values in the template-matching differential expression analysis.

Value

data frame; the population, fold change (fc), mean p, mean np, p-value, p-value adjusted, and gene.

edroaldo/fusca documentation built on March 1, 2023, 1:43 p.m.