getCMstats {TFEA.ChIP} | R Documentation |
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.
getCMstats(contMatrix_list, chip_index = get_chip_index())
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 |
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).
data('CM_list',package = 'TFEA.ChIP') stats_mat_UP <- getCMstats(CM_list)