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Fix output dir usage

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This commit is contained in:
Bryan Roessler
2024-09-01 18:50:47 -04:00
parent f1cc7b8404
commit 79175e7821
1 changed files with 4 additions and 4 deletions
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8
workflow/apps/r/calculate_interaction_zscores5.R
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@@ -306,7 +306,7 @@ calculate_bg_means <- function(df_stats_by_l, df_stats_by_k, df_stats_by_r, df_s
} }
# Process strains (deletion and reference) # Process strains (deletion and reference)
process_strains <- function(df, l_within_2sd_k, strain, output_dir) { process_strains <- function(df, l_within_2sd_k, strain) {
df_strains <- data.frame() # Initialize an empty dataframe to store results df_strains <- data.frame() # Initialize an empty dataframe to store results
for (concentration in unique(df$conc_num)) { for (concentration in unique(df$conc_num)) {
@@ -627,7 +627,7 @@ main <- function() {
stats_by_r_bg <- stats_bg %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_r_bg <- stats_bg %>% select(starts_with("r_"), "OrfRep", "conc_num", "conc_num_factor")
stats_by_auc_bg <- stats_bg %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor") stats_by_auc_bg <- stats_bg %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor")
write.csv(stats_bg, write.csv(stats_bg,
file = file.path(output_dir, paste0("SummaryStats_BackgroundStrains_", strain, ".csv")), file = file.path(out_dir, paste0("SummaryStats_BackgroundStrains_", strain, ".csv")),
row.names = FALSE) row.names = FALSE)
stats_bg_joined <- left_join(df_bg, stats_bg, by = c("conc_num", "conc_num_factor")) stats_bg_joined <- left_join(df_bg, stats_bg, by = c("conc_num", "conc_num_factor"))
@@ -666,9 +666,9 @@ main <- function() {
mutate(SM = 0) mutate(SM = 0)
message("Processing reference strain") message("Processing reference strain")
reference_strain <- process_strains(df_reference, l_within_2sd_k, strain, out_dir) reference_strain <- process_strains(df_reference, l_within_2sd_k, strain)
message("Processing deletion strains") message("Processing deletion strains")
deletion_strains <- process_strains(df_deletion, l_within_2sd_k, strain, out_dir) deletion_strains <- process_strains(df_deletion, l_within_2sd_k, strain)
# Deprecated # Deprecated
# Change OrfRep to include the reference strain, gene, and Num so each RF gets its own score # Change OrfRep to include the reference strain, gene, and Num so each RF gets its own score