identifyAC: Identification of the Abundant Clusters

In tchitchek-lab/SPADEVizR: SPADEVizR: an R package for Visualization, Analysis and Integration of SPADE results

Identification of the Abundant Clusters

Description

This function is used to identify the Abundant Clusters (AC), that is to say clusters having cell abundance (absolute or relative) statistically greater than a specific threshold. Abundant Clusters are identified using a one-sample test (parametrized or non-parametrized). P-values can be corrected for multiple comparisons.

Usage

identifyAC(Results, samples, use.percentages = TRUE, method = "t.test",
  method.adjust = NULL, mu = 0, th.pvalue = 0.05)

Arguments

Results	a 'Results' object
samples	a character vector providing the sample names to used
use.percentages	a logical specifying if the computations should be performed on percentage
method	a character specifying the statistical method used to identify the Abundant Clusters. The parameter can take the values "t.test" or "wilcox.test"
method.adjust	a character specifying if the p-values should be corrected using multiple correction methods among: "holm", "hochberg", "hommel", "bonferroni", "BH", "BY" and "fdr" (from 'stats::p.adjust' method)
mu	a numeric specifying the theoretical value (mu) of the one sample statistical test
th.pvalue	a numeric specifying the p-value threshold

Value

a S4 object of class 'AC'

tchitchek-lab/SPADEVizR documentation built on Jan. 27, 2024, 8:58 p.m.