contingency_matrix: Computes 2x2 contingency matrices

In TFEA.ChIP: Analyze Transcription Factor Enrichment

Description

Function to compute contingency 2x2 matrix by the partition of the two gene ID lists according to the presence or absence of the terms in these list in a ChIP-Seq binding database.

Usage

contingency_matrix(test_list, control_list,
  chip_index = get_chip_index())

Arguments

test_list	List of gene Entrez IDs
control_list	If not provided, all human genes not present in test_list will be used as control.
chip_index	Output of the function <e2><80><9c>get_chip_index<e2><80><9d>, 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

List of contingency matrices, one CM per element in chip_index (i.e. per ChIP-seq dataset).

Examples

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

TFEA.ChIP documentation built on Nov. 8, 2020, 5:05 p.m.