From e1d868e728dfe8615a1d206680ace9c848af61a8 Mon Sep 17 00:00:00 2001 From: Candace Savonen Date: Fri, 23 Aug 2024 13:24:12 -0400 Subject: [PATCH] Delete design matrix part for now --- R/00-setup_data.R | 32 -------------------------------- 1 file changed, 32 deletions(-) diff --git a/R/00-setup_data.R b/R/00-setup_data.R index 1a8489b..a9de3da 100644 --- a/R/00-setup_data.R +++ b/R/00-setup_data.R @@ -1,35 +1,3 @@ -#' Specify a design matrix -#' @description This function allows people to have their data ready to be processed by gimap -#' @param counts a matrix of data that contains the counts where rows are each paired_guide target and columns are each sample -#' @param pg_ids the pgRNA IDs: metadata associated with the pgRNA constructs that correspond to the rows of the counts data -#' @param pg_metadata construct metadata -#' @param sample_metadata metadata associated with the samples of the dataset that correspond to the columns of the counts data. -#' Should include a column that has replicate information as well as a column that contains timepoint information respectively (this will be used for log fold calculations). These columns should be factors. -#' @return A special gimap_dataset to be used with the other functions in this package. -#' @export -#' @examples \dontrun{ -#' -#' example_counts <- get_example_data("count") %>% -#' dplyr::select(c("Day00_RepA", "Day05_RepA", "Day22_RepA", "Day22_RepB", "Day22_RepC")) %>% -#' as.matrix() -#' -#' example_sample_metadata <- data.frame( -#' col_names = c("Day00_RepA", "Day05_RepA", "Day22_RepA", "Day22_RepB", "Day22_RepC"), -#' day = as.numeric(c("0", "5", "22", "22", "22")), -#' rep = as.factor(c("RepA", "RepA", "RepA", "RepB", "RepC")) -#' ) -#' -#' model.matrix(~day + rep, data = example_sample_metadata) -#' -#' gimap_dataset <- setup_data(counts = example_counts, -#' design_matrix = ) -#' } -#' -#' -#' - - - #' Making a new gimap dataset #' @description This function allows people to have their data ready to be processed by gimap