Add data sets

NAMESPACE

@@ -1,5 +1,11 @@
 # Generated by roxygen2: do not edit by hand
 
+export(copy_csv)
 export(copy_expt)
 export(copy_frac)
-export(copy_globalCPTAC)
+export(cptac_csv_1)
+export(cptac_csv_2)
+export(cptac_expt_1)
+export(cptac_expt_2)
+export(cptac_frac_1)
+export(cptac_frac_2)

R/globalCPTAC.R

@@ -1,48 +1,98 @@
 #' Copy Mascot \code{.csv} files
 #'
-#' \code{copy_globalCPTAC} copies the \code{.csv} files from Mascot searches to
-#' a target directory.
+#' \code{copy_dat} copies the Mascot outputs of \code{.csv} files to a target
+#' directory.
 #' @export
-copy_globalCPTAC <- function(dat_dir) {
+copy_csv <- function(dat_dir, filelist) {
   dir.create(file.path(dat_dir), recursive = TRUE, showWarnings = FALSE)
 
-  filelist <- c("F003481", "F003485", "F003486", "F003487", "F003488", "F003510")
   data(list = filelist, package = "proteoQDA", envir = environment())
 
   for (i in seq_along(filelist)) {
     fileConn <- file(file.path(dat_dir, paste0(filelist[i], ".csv")))
     df <- get(filelist[i])
-
     writeLines(df, fileConn)
     close(fileConn)
   }
 }
 
 
+#' Copy Mascot \code{.csv} files
+#'
+#' @export
+cptac_csv_1 <- function(dat_dir) {
+	copy_csv(dat_dir, filelist = c("F003481", "F003485", "F003486", "F003487", "F003488", "F003510"))
+}
+
+
+#' Copy Mascot \code{.csv} files
+#'
+#' @export
+cptac_csv_2 <- function(dat_dir) {
+  copy_csv(dat_dir, filelist = c("F003529", "F003530", "F003531", "F003532", "F003533", "F003534"))
+}
+
+
+
 #' Copy \code{expt_smry.xlsx}
 #'
 #' \code{copy_expt} copies the \code{expt_smry.xlsx} to a target directory.
 #' @export
-copy_expt <- function(dat_dir) {
+copy_expt <- function(dat_dir, filename = "expt_smry.xlsx") {
   dir.create(file.path(dat_dir), recursive = TRUE, showWarnings = FALSE)
 
-  filepath <- system.file("extdata", "expt_smry.xlsx", package = "proteoQ")
-  if (nchar(filepath) == 0) stop("Load `library(proteoQ)` first.")
+  filepath <- system.file("extdata", filename, package = "proteoQDA")
+  # if (nchar(filepath) == 0) stop("Load `library(proteoQ)` first.")
   filepath <- gsub("/", "\\\\", filepath)
   file.copy(from = filepath, to = file.path(dat_dir, "expt_smry.xlsx"))
 }
 
 
+#' Copy \code{expt_smry.xlsx}
+#'
+#' @export
+cptac_expt_1 <- function(dat_dir) {
+  copy_expt(dat_dir, "expt_smry_cptac_gl.xlsx")
+}
+
+
+#' Copy \code{expt_smry.xlsx}
+#'
+#' @export
+cptac_expt_2 <- function(dat_dir) {
+  copy_expt(dat_dir, "expt_smry_cptac_cmbn.xlsx")
+}
+
+
+
 #' Copy \code{frac_smry.xlsx}
 #'
-#' \code{copy_frac} copies the \code{expt_smry.xlsx} to a target directory.
+#' \code{copy_frac} copies the \code{frac_smry.xlsx} to a target directory.
 #' @export
-copy_frac <- function(dat_dir) {
+copy_frac <- function(dat_dir, filename = "frac_smry.xlsx") {
   dir.create(file.path(dat_dir), recursive = TRUE, showWarnings = FALSE)
 
-  filepath <- system.file("extdata", "frac_smry.xlsx", package = "proteoQ")
-  if (nchar(filepath) == 0) stop("Load `library(proteoQ)` first.")
+  filepath <- system.file("extdata", filename, package = "proteoQDA")
+  # if (nchar(filepath) == 0) stop("Load `library(proteoQ)` first.")
   filepath <- gsub("/", "\\\\", filepath)
   file.copy(from = filepath, to = file.path(dat_dir, "frac_smry.xlsx"))
 }
 
+
+#' Copy \code{frac_smry.xlsx}
+#'
+#' @export
+cptac_frac_1 <- function(dat_dir) {
+  copy_frac(dat_dir, "frac_smry_cptac_gl.xlsx")
+}
+
+
+#' Copy \code{frac_smry.xlsx}
+#'
+#' @export
+cptac_frac_2 <- function(dat_dir) {
+  copy_frac(dat_dir, "frac_smry_cptac_cmbn.xlsx")
+}
+
+
+