R/krsa_get_diff.R

In CogDisResLab/KRSA: KRSA: Kinome Random Sampling Analyzer

#' Extract differential peptides based on LFC cutoff
#'
#' This function takes in the LFC table, column name, and an LFC cutoff to extracts differentially phosphorylated peptides
#'
#' @param data LFC table
#' @param col LFC column name
#' @param lfc_thr LFC cutoffs
#' @param sd_thr SD cutoff
#'
#' @return peptides
#'
#' @family helper functions
#'
#'
#' @export
#'
#' @examples
#' TRUE
krsa_get_diff <- function(data, col, lfc_thr, sd_thr = Inf) {
    peplist <- vector("list", length(lfc_thr))
    for (i in 1:length(lfc_thr)) {
        dplyr::filter(data, {{ col }} >= lfc_thr[i] | {{ col }} <= lfc_thr[i] * -1) %>%
            dplyr::filter(LFC_SD <= sd_thr | is.na(LFC_SD)) %>%
            dplyr::pull(Peptide) %>%
            unique() -> peplist[[i]]
    }
    names(peplist) <- as.character(lfc_thr)
    peplist
}