get_chip_index: Creates df containing accessions of ChIP-Seq datasets and TF.

In TFEA.ChIP: Analyze Transcription Factor Enrichment

Description

Function to create a data frame containing the ChIP-Seq dataset accession IDs and the transcription factor tested in each ChIP. This index is used in functions like <e2><80><9c>contingency_matrix<e2><80><9d> and <e2><80><9c>GSEA_run<e2><80><9d> as a filter to select specific ChIPs or transcription factors to run an analysis.

Usage

get_chip_index(encodeFilter = FALSE, TFfilter = NULL)

Arguments

encodeFilter	(Optional) If TRUE, only ENCODE ChIP-Seqs are included in the index.
TFfilter	(Optional) Transcription factors of interest.

Value

Data frame containig the accession ID and TF for every ChIP-Seq experiment included in the metadata files.

Examples

get_chip_index(encodeFilter = TRUE)
get_chip_index(TFfilter=c('SMAD2','SMAD4'))

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