getCMstats: Generate statistical parameters from a contingency_matrix...

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Generate statistical parameters from a contingency_matrix output

Description

From a list of contingency matrices, such as the output from “contingency_matrix”, this function computes a fisher's exact test for each matrix and generates a data frame that stores accession ID of a ChIP-Seq experiment, the TF tested in that experiment, the p-value and the odds ratio resulting from the test.

Usage

getCMstats(CM_list, chip_index = get_chip_index())

Arguments

CM_list	Output of “contingency_matrix”, a list of contingency matrices.
chip_index	Output of the function “get_chip_index”, a data frame containing accession IDs of ChIPs on the database and the TF each one tests. If not provided, the whole internal database will be used

Value

Data frame containing accession ID of a ChIP-Seq experiment and its experimental conditions, the TF tested in that experiment, raw and adjusted p-values, odds-ratio, and euclidean distance. and FDR-adjusted p-values (-10*log10 adj.pvalue).

Examples

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

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