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

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Rank the TFs in the output from 'getCMstats'

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('Genes.Upreg',package = 'TFEA.ChIP')
CM_list_UP <- contingency_matrix(Genes.Upreg)
stats_mat_UP <- getCMstats(CM_list_UP)
rankTFs( stats_mat_UP )

LauraPS1/TFEA.ChIP documentation built on April 21, 2023, 7:29 a.m.