From 02cbcdd484e76565011e02df434f1998d8d3415c Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Fri, 29 Jan 2021 22:42:22 +0000 Subject: [PATCH 1/3] Reduce title name (under 65 characters) --- DESCRIPTION | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b107611..282a9a6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,6 @@ Package: MetaPipe Type: Package -Title: A High-Performance Computing Pipeline for QTL Mapping of Large Ionomic - and Metabolomic Datasets +Title: A High-Performance Computing Pipeline for QTL Mapping Version: 0.1.0 Authors@R: c( person(given = "Roberto", From f0d2d395227f4e6d777054aa0039b29b969b488f Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Fri, 29 Jan 2021 22:47:27 +0000 Subject: [PATCH 2/3] Update return documentation for effect_plots --- R/utils-qtl.R | 1 + 1 file changed, 1 insertion(+) diff --git a/R/utils-qtl.R b/R/utils-qtl.R index 442ede5..e211384 100644 --- a/R/utils-qtl.R +++ b/R/utils-qtl.R @@ -100,6 +100,7 @@ transform_pseudo_marker <- function(x_data, marker, chr, pos) { #' @param cpus Number of CPUs to be used in the computation. #' @param plots_dir Output directory for plots. #' +#' @return Effect plots (PNG files) for each trait-marker combination. #' @export #' #' @examples From 84752744d35af7be1a9c7af819085bfcfebd1cea Mon Sep 17 00:00:00 2001 From: Roberto Villegas-Diaz Date: Fri, 29 Jan 2021 22:50:54 +0000 Subject: [PATCH 3/3] Export tidy_up --- R/utils.R | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/R/utils.R b/R/utils.R index cf2837c..d6f0fba 100644 --- a/R/utils.R +++ b/R/utils.R @@ -163,10 +163,9 @@ rplc_na <- function(x) { #' List files matching a pattern and delete them #' #' @param patterns Vector of strings with patterns to be deleted. -#' @param path Path to the directory containing the files +#' @param path Path to the directory containing the files. #' -#' @keywords internal -#' @noRd +#' @export tidy_up <- function(patterns, path = here::here()) { # List files filenames <- unlist(lapply(patterns,