R/junc_addcols.R

In DanielRivasMD/Rpack.chlSab: chlSab Vervet green monkey

#' @title Junction Additional Columns
#'
#' @description
#' Description
#'
#' @param fi_link Project enviorment option
#' @param fi_tmp_peak_ls Project enviorment option
#' @param up_junc_pos Project enviorment option
#' @param down_junc_pos Project enviorment option
#' @param gie_sum_names Project enviorment option
#'
#' @return
#' Return
#'
#' @seealso \code{peak_linker}
#' @export

junc_addcols <- function(

	fi_link,
	fi_tmp_peak_ls,
	up_junc_pos,
	down_junc_pos,
	gie_sum_names
) {

	f_up_junc_pos <- match(
		fi_link[which(!is.na(fi_link$dist)), "Positions"],
		fi_tmp_peak_ls[[which(gie_sum_names == up_junc_pos)]][, "upper_lim_nt"]
	)

	f_down_junc_pos <- match(
		fi_link[which(is.na(fi_link$dist)), "Positions"],
		fi_tmp_peak_ls[[which(gie_sum_names == down_junc_pos)]][, "lower_lim_nt"]
	)

	fi_tmp_peak_ls[[which(gie_sum_names == up_junc_pos)]][f_up_junc_pos, "dist_nt"] <- fi_link[which(!is.na(fi_link$dist)), "dist"]
	fi_tmp_peak_ls[[which(gie_sum_names == up_junc_pos)]][f_up_junc_pos, "link_inner_edge"] <- fi_link[which(is.na(fi_link$dist)), "Positions"]
	fi_tmp_peak_ls[[which(gie_sum_names == up_junc_pos)]][f_up_junc_pos, "link_no"] <- f_down_junc_pos
	fi_tmp_peak_ls[[which(gie_sum_names == up_junc_pos)]][f_up_junc_pos, "global_link_no"] <- fi_tmp_peak_ls[[which(gie_sum_names == down_junc_pos)]][f_down_junc_pos, "global_no"]

	fi_tmp_peak_ls[[which(gie_sum_names == down_junc_pos)]][f_down_junc_pos, c("link_inner_edge", "dist_nt")] <- fi_link[which(!is.na(fi_link$dist)), c("Positions", "dist")]
	fi_tmp_peak_ls[[which(gie_sum_names == down_junc_pos)]][f_down_junc_pos, "link_no"] <- f_up_junc_pos
	fi_tmp_peak_ls[[which(gie_sum_names == down_junc_pos)]][f_down_junc_pos, "global_link_no"] <- fi_tmp_peak_ls[[which(gie_sum_names == up_junc_pos)]][f_up_junc_pos, "global_no"]

	return(list(
		fi_tmp_peak_ls[[which(gie_sum_names == up_junc_pos)]],
		fi_tmp_peak_ls[[which(gie_sum_names == down_junc_pos)]]
	))
}