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:

- 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 )

[Package TFEA.ChIP version 1.12.0 Index]