identifyDAC: Identification of the Differentially Abundant Clusters

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

Identification of the Differentially Abundant Clusters

Description

This function is used to identify differentially abundant clusters, that is to say clusters having abundance (absolute or relative) statistically different between two biological conditions. Differentially Abundant Clusters are identified using a two-sample test (parametrized or non-parametrized). P-values can be corrected for multiple comparisons.

Usage

identifyDAC(Results, condition1, condition2, use.percentages = TRUE,
  method = "t.test", method.adjust = NULL, method.paired = FALSE,
  th.pvalue = 0.05, th.fc = 2)

Arguments

Results	a 'Results' object
condition1	a character vector providing the sample names defined as the first condition
condition2	a character vector providing the sample names defined as the second condition
use.percentages	a logical specifying if the computations should be performed on percentage
method	a character specifying the name of the statistical test to use "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)
method.paired	a logical indicating if the statistical test must be performed in a paired manner
th.pvalue	a numeric specifying the p-value threshold
th.fc	a numeric specifying the fold-change threshold

Value

a S4 object of class 'DAC'

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