matrixDB_to_listDB: Re-formatting ChIP-Gene database

In LauraPS1/TFEA.ChIP: Analyze Transcription Factor Enrichment

Re-formatting ChIP-Gene database

Description

Function to transform a ChIP-gene data base from the former binary matrix to the current list-based format.

Usage

matrixDB_to_listDB(Mat01)

Arguments

Mat01

Matrix[n,m] which rows correspond to all the human genes that have been assigned an Entrez ID, and its columns, to every ChIP-Seq experiment in the database. The values are 1 – if the ChIP-Seq has a peak assigned to that gene – or 0 – if it hasn’t –.

Value

List containing two elements: - Gene Keys: vector of gene IDs - ChIP Targets: list of vectors, one per ChIP-seq experiment in the, database, containing the putative targets assigned. Each target is coded as its position in the vector 'Gene Keys'.

Examples

Mat01 <- matrix( 
    round( runif(9) ), nrow = 3,
    dimnames= list( paste0("Gene ", 1:3), paste0("ChIPseq ", 1:3))  )
matrixDB_to_listDB( Mat01 )

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