get_chip_index {TFEA.ChIP} | R Documentation |
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 “contingency_matrix” and “GSEA_run” as a filter to select specific ChIPs or transcription factors to run an analysis.
get_chip_index(encodeFilter = FALSE, TFfilter = NULL)
encodeFilter |
(Optional) If TRUE, only ENCODE ChIP-Seqs are included in the index. |
TFfilter |
(Optional) Transcription factors of interest. |
Data frame containig the accession ID and TF for every ChIP-Seq experiment included in the metadata files.
get_chip_index(encodeFilter = TRUE) get_chip_index(TFfilter=c('SMAD2','SMAD4'))