R/peak_extract.R

In DanielRivasMD/Rpack.chlSab: chlSab Vervet green monkey

#' @title Peak Extract
#'
#' @description
#' Description
#'
#' @param f_data data.frame
#' @param f_col Column to extract from
#' @param ge_strands Project Global Enviorment option
#' @param ge_junctions Project Global Enviorment option
#' @param ge_str_tag Project Global Enviorment option
#' @param ge_sum_names Project Global Enviorment option
#'
#' @return
#' Return
#'
#' @export

peak_extract <- function(

	f_data,
	f_col,
	ge_strands,
	ge_junctions,
	ge_str_tag,
	ge_sum_names
) {

	f_peak_ls <- list()
	for(f_str in seq_along(ge_strands)){
		#
		for(f_junc in seq_along(ge_junctions)){
			#
			f_int_str <- which(paste0(ge_strands[f_str], ge_junctions[f_junc]) == ge_sum_names)
			#
			f_peak_ls[[f_int_str]] <- CopperGenomicFunctions::peak_iden(
				CopperGenomicFunctions::dec_tag(
					f_data[, f_col],
					ge_str_tag[f_int_str]
				)
			)
			f_peak_ls[[f_int_str]]$Orientation <- ge_sum_names[f_int_str]
		}
	}
	peak_coor <- tibble::as_tibble( (CopperGenomicFunctions::concat_ls(f_peak_ls)) )

	return()
}