R/epiRomics_enhanceosome.R

In Huising-Lab/epiRomics: Epigenomic Analysis Package Built for R (epiRomics)

#' Identifies putative enhanceosome regions by cross-referencing candidate enhancer regions against co-TF enrichment
#'
#' @param epiRomics_putative_enhancers epiRomics class database containing putative enhancer calls
#' @param epiRomics_dB epiRomics class database containing all data initially loaded
#' @return Variable of class epiRomics further exploring candidate enhanceosome regions using co-ChIP hits
#' @export
epiRomics_enhanceosome <- function(epiRomics_putative_enhancers, epiRomics_dB) {
  epiRomics_chips <- epiRomics_dB@meta[epiRomics_dB@meta$type == "chip", "name"]
  epiRomics_chips_db_access <- base::paste0(epiRomics_dB@genome, "_custom_", epiRomics_chips)
  epiRomics_enhanceosome_data_table <- base::matrix(ncol = base::length(epiRomics_chips), nrow = base::length(epiRomics_putative_enhancers@annotations))
  base::colnames(epiRomics_enhanceosome_data_table) <- epiRomics_chips
  for (c in 1:base::length(epiRomics_chips)) {
    epiRomics_enhanceosome_data_table[, c] <- GenomicRanges::countOverlaps(
      epiRomics_putative_enhancers@annotations,
      epiRomics_dB@annotations[epiRomics_dB@annotations$type == epiRomics_chips_db_access[c], ]
    )
  }
  epiRomics_enhanceosome_data_table <- base::cbind(epiRomics_enhanceosome_data_table,
    ChIP_Hits = base::rowSums(epiRomics_enhanceosome_data_table),
    base::as.data.frame(epiRomics_putative_enhancers@annotations)
  )

  epiRomics_enhanceosome_data_table <- epiRomics_enhanceosome_data_table[base::order(epiRomics_enhanceosome_data_table$ChIP_Hits,
    decreasing = TRUE
  ), ]
  epiRomics_enhanceosome_data_table <- GenomicRanges::GRanges(epiRomics_enhanceosome_data_table)
  epiRomics_enhanceosome_data_table_annotated <- ChIPseeker::annotatePeak(epiRomics_enhanceosome_data_table,
    tssRegion = c(-3000, 3000), TxDb = base::eval(base::parse(text = epiRomics_dB@txdb)), annoDb = epiRomics_dB@organism
  )
  epiRomics_enhanceosome_data_table_annotated <- epiRomics_enhanceosome_data_table_annotated@anno
  epiRomics_enhanceosome <- epiRomics_putative_enhancers
  epiRomics_enhanceosome@annotations <- epiRomics_enhanceosome_data_table_annotated
  base::return(epiRomics_enhanceosome)
}