identifyCC: Identification of the correlation of SPADE cluster with a...

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

Identification of the correlation of SPADE cluster with a phenotype

Description

This function is used to identify Correlated Clusters, that is to say clusters having an abundance (absolute or relative) statistically correlated with a biological variable. Correlated Clusters are identified using Pearson or Spearman coefficients of correlation. P-values can be corrected for multiple comparisons.

Usage

identifyCC(Results, variable, use.percentages = TRUE,
  method = "pearson", method.adjust = NULL, th.correlation = 0.75,
  th.pvalue = 0.05)

Arguments

Results	a 'Results' object
variable	a numerical named vector providing the correspondence between a sample name (in rownames) and the specific numerical phenotype
use.percentages	a logical specifying if the computations should be performed on percentage
method	a character indicating the correlation method to use: "pearson", "spearman"
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)
th.correlation	a numeric specifying the absolute value of the correlation coefficient threshold
th.pvalue	a numeric specifying the p-value threshold

Value

a S4 object of class 'CC'

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