rankTFs {TFEA.ChIP} | R Documentation |
Rank the TFs in the output from 'getCMstats' using Wilcoxon rank-sum test or a GSEA-like approach.
rankTFs( resultsTable, rankMethod = "gsea", makePlot = FALSE, plotTitle = "TF ranking" )
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. |
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
data('Genes.Upreg',package = 'TFEA.ChIP') CM_list_UP <- contingency_matrix(Genes.Upreg) stats_mat_UP <- getCMstats(CM_list_UP) rankTFs( stats_mat_UP )