From 9e2a2d16c54ec926c66de5a8d4946b0d86d902a7 Mon Sep 17 00:00:00 2001 From: Bryan Roessler Date: Sun, 1 Sep 2024 03:34:22 -0400 Subject: [PATCH] Replace sgd_genes function with vectorized approach --- workflow/apps/r/calculate_interaction_zscores5.R | 12 ------------ 1 file changed, 12 deletions(-) diff --git a/workflow/apps/r/calculate_interaction_zscores5.R b/workflow/apps/r/calculate_interaction_zscores5.R index 492c7a7e..08a1fbe9 100644 --- a/workflow/apps/r/calculate_interaction_zscores5.R +++ b/workflow/apps/r/calculate_interaction_zscores5.R @@ -99,15 +99,6 @@ scale_colour_publication <- function(...) { )), ...) } -# Load SGD gene list -sgd_genes <- function(sgd_gene_list) { - read.delim(file = sgd_gene_list, quote = "", header = FALSE, - colClasses = c(rep("NULL", 3), rep("character", 2), rep("NULL", 11))) %>% - dplyr::rename(ORF = V4, GeneName = V5) -} - -genes <- sgd_genes(args$sgd_gene_list) - # Load the initial dataframe from the easy_results_file load_and_process_data <- function(easy_results_file, sd = 3) { df <- read.delim(easy_results_file, skip = 2, as.is = TRUE, row.names = 1, strip.white = TRUE) @@ -299,7 +290,6 @@ process_strains <- function(df, l_within_2sd_k, strain, output_dir) { return(df_strains) } - calculate_interaction_scores <- function(df, df_stats_by_l, df_stats_by_k, df_stats_by_r, df_stats_by_auc, background_means, max_conc, variables, group_vars = c("OrfRep", "Gene", "num")) { @@ -437,7 +427,6 @@ generate_cpp_correlation_plots <- function(df_na_rm, lm_list, output_dir) { save_plots("Correlation_CPPs", plot_list, output_dir) } - # Adjust missing values and calculate ranks adjust_missing_and_rank <- function(df) { df <- df %>% @@ -511,7 +500,6 @@ create_ranked_plots <- function(df, output_dir) { generate_and_save_ranked_plots(df_adjusted, output_dir, "RankPlots_lm_naRM") } - main <- function() { # Applying to all experiments lapply(names(args$experiments), function(exp_name) {