getCMstats {TFEA.ChIP} | R Documentation

## 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(contMatrix_list, chip_index = get_chip_index())

### Arguments

`contMatrix_list` | Output of “contingency_matrix”, a list of contingency matrix.
`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)

[Package TFEA.ChIP version 1.12.0 Index]