compareTwoGroups-methods: Compute fold changes and find gene signatures.

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

Compute fold changes and find gene signatures.

Description

Compute mean expression of each gene in two populations and compares them using fold changes, p-value of wilcox test and adjusted p-value using the bonferroni method.

Usage

compareTwoGroups(
  object,
  assay.type = "RNA",
  column = "population",
  group1,
  group2,
  fc.threshold = 0.25
)

## S4 method for signature 'CellRouter'
compareTwoGroups(
  object,
  assay.type = "RNA",
  column = "population",
  group1,
  group2,
  fc.threshold = 0.25
)

Arguments

object	CellRouter object.
assay.type	character; the type of data to use.
column	character; column in the metadata table to group cells for differential expression. For example, if 'population' is specified, population-specific gene signatures will be identified.
group1	character; name of group 1 used in comparison.
group2	character; name of group 2 used in comparison.
fc.threshold	numeric; fold change threshold.

Value

data frame; a data frame with the mean expression of the genes in group 1 (p column), the mean expression of the genes in group 2 (np column), the fold changes (fc column), the p-value for the wilcox test (pv column), and the adjusted p-value (p.adj column).

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