R/webgestalt.R

In ge11232002/OlinkR: A toolkit for Olink data analysis

#' Produce files for webgestalt website
#'
#' Given a \code{tibble} object of the results returned from \code{olink_limma} function, generate the files for upload to webgestalt website.
#'
#' @param x A \code{tibble} object from \code{olink_limma} function.
#' @param pvalue The p-value to filter for significant proteins. The default is 0.01.
#' @param log2FC The log2 fold change cut-off to filter for significant proteins. The default is 0, i.e. no filtering.
#' @param dir The output folder. The default is current working directory.
#' @importFrom readr write_lines write_tsv
#' @importFrom dplyr filter pull select
#' @importFrom rlang .data
#' @importFrom fs dir_create path
#' @export
#' @return An invisible character object with exported file names.
#' @author Ge Tan
#' @examples
#' npxFn <- system.file("extdata",
#'                       c("20200507_Inflammation_NPX_1.xlsx",
#'                         "20200625_Inflammation_NPX_2.xlsx"),
#'                      package = "OlinkR")
#' metaFn <- system.file("extdata", "Inflammation_Metadata.xlsx", package = "OlinkR")
#' se <- as_se(read_npx(npxFn, metaFn))
#' tb <- olink_limma(se, factorCol = "condition_Factor",
#'                   contrasts = "Glucose.10mM.Vehicle - Vehicle.Vehicle",
#'                   blocking = "Donor_Factor")
#' files <- webgestalt_prep(tb)
#' file.remove(files)
webgestalt_prep <- function(x, pvalue = 0.01, log2FC = 0, dir = ".") {
  dir_create(dir)

  # ORA files ---------------------------------------------------------------
  tb_ora <- x %>%
    filter(.data$logFC > log2FC, .data$P.Value <= pvalue) %>%
    pull(.data$UniProt)
  write_lines(tb_ora, file = path(dir, "webgestalt_upregulated_ora.txt"))

  tb_ora <- x %>%
    filter(.data$logFC < -log2FC, .data$P.Value <= pvalue) %>%
    pull(.data$UniProt)
  write_lines(tb_ora, file = path(dir, "webgestalt_downregulated_ora.txt"))

  # GSEA --------------------------------------------------------------------
  tb_gsea <- x %>%
    select(.data$UniProt, .data$logFC)
  write_tsv(tb_gsea, file = path(dir, "webgestalt_gsea.rnk"),
            col_names = FALSE)

  # Background --------------------------------------------------------------
  tb_background <- x %>%
    pull(.data$UniProt)
  write_lines(tb_background, file = path(dir, "webgestalt_background.txt"))

  invisible(path(dir,
                 c("webgestalt_upregulated_ora.txt",
                   "webgestalt_downregulated_ora.txt",
                   "webgestalt_gsea.rnk", "webgestalt_background.txt")
                 )
            )
}