rankTFs: Rank the TFs in the output from 'getCMstats'

In TFEA.ChIP: Analyze Transcription Factor Enrichment

Description

Rank the TFs in the output from 'getCMstats' using Wilcoxon rank-sum test or a GSEA-like approach.

Usage

rankTFs(resultsTable, rankMethod = "gsea", makePlot = FALSE,
  plotTitle = "TF ranking")

Arguments

resultsTable	Output from the function 'getCMstats'
rankMethod	"wilcoxon" or "gsea".
makePlot	(Optional) For rankMethod="gsea". If TRUE, generates a plot for TFs with a p-value < 0.05.
plotTitle	(Optional) Title for the plot.

Value

data frame containing:

• For Wilcoxon rank-sum test: rank, TF name, test statistic ('wilc_W), p-value, Freeman's theta, epsilon-squared anf effect size

• For GSEA-like ranking: TF name, enrichment score, argument, p-value, number of ChIPs

Examples

data('stat_mat',package = 'TFEA.ChIP')
rankTFs( stat_mat )

TFEA.ChIP documentation built on Nov. 8, 2020, 5:05 p.m.