rankTFs {TFEA.ChIP}R Documentation

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:

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 )

[Package TFEA.ChIP version 1.13.0 Index]