bryan/hartman-server
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

Fix output dir usage

Browse Source
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
Download Patch File Download Diff File Expand all files Collapse all files

8
workflow/apps/r/calculate_interaction_zscores5.R
View File

@@ -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 <- 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
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_auc_bg <- stats_bg %>% select(starts_with("AUC_"), "OrfRep", "conc_num", "conc_num_factor")
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)
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)
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")
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
# Change OrfRep to include the reference strain, gene, and Num so each RF gets its own score