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No destructuring in base R

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Bryan Roessler
2024-09-05 20:45:44 -04:00
parent de599ed5b8
commit 5808311e49
1 changed files with 12 additions and 9 deletions
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21
workflow/apps/r/calculate_interaction_zscores5.R
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@@ -638,8 +638,9 @@ main <- function() {
# Calculate summary statistics # Calculate summary statistics
message("Calculating summary statistics for all strains") message("Calculating summary statistics for all strains")
variables <- c("L", "K", "r", "AUC") variables <- c("L", "K", "r", "AUC")
list(summary_stats, df_na_stats) <- calculate_summary_stats(df_na, variables, group_vars = c("OrfRep", "conc_num", "conc_num_factor")) ss <- calculate_summary_stats(df_na, variables, group_vars = c("OrfRep", "conc_num", "conc_num_factor"))
# stats <- calculate_summary_stats(df_na, variables, group_vars = c("OrfRep", "conc_num", "conc_num_factor")) summary_stats <- ss$summary_stats
df_na_stats <- ss$df_with_stats
write.csv(summary_stats, file = file.path(out_dir, "SummaryStats_ALLSTRAINS.csv"), row.names = FALSE) write.csv(summary_stats, file = file.path(out_dir, "SummaryStats_ALLSTRAINS.csv"), row.names = FALSE)
print("Summary stats:") print("Summary stats:")
@@ -657,12 +658,13 @@ main <- function() {
# Summary statistics for within and outside 2SD of K # Summary statistics for within and outside 2SD of K
message("Calculating summary statistics for L within 2SD of K") message("Calculating summary statistics for L within 2SD of K")
list(l_within_2sd_k_stats, df_na_l_within_2sd_k_stats) <- ss <- calculate_summary_stats(df_na_within_2sd_k, "L", group_vars = c("conc_num", "conc_num_factor"))
calculate_summary_stats(df_na_l_within_2sd_k, "L", group_vars = c("conc_num", "conc_num_factor")) l_within_2sd_k_stats <- ss$summary_stats
df_na_l_within_2sd_k_stats <- ss$df_with_stats
message("Calculating summary statistics for L outside 2SD of K") message("Calculating summary statistics for L outside 2SD of K")
list(l_outside_2sd_k_stats, df_na_l_outside_2sd_k_stats) <- ss <- calculate_summary_stats(df_na_outside_2sd_k, "L", group_vars = c("conc_num", "conc_num_factor"))
calculate_summary_stats(df_na_outside_2sd_k, "L", group_vars = c("conc_num", "conc_num_factor")) l_outside_2sd_k_stats <- ss$summary_stats
df_na_l_outside_2sd_k_stats <- ss$df_with_stats
# Write CSV files # Write CSV files
write.csv(l_within_2sd_k_stats, file = file.path(out_dir_qc, "Max_Observed_L_Vals_for_spots_within_2sd_k.csv"), row.names = FALSE) write.csv(l_within_2sd_k_stats, file = file.path(out_dir_qc, "Max_Observed_L_Vals_for_spots_within_2sd_k.csv"), row.names = FALSE)
write.csv(l_outside_2sd_k_stats, file = file.path(out_dir, "Max_Observed_L_Vals_for_spots_outside_2sd_k.csv"), row.names = FALSE) write.csv(l_outside_2sd_k_stats, file = file.path(out_dir, "Max_Observed_L_Vals_for_spots_outside_2sd_k.csv"), row.names = FALSE)
@@ -687,8 +689,9 @@ main <- function() {
# Recalculate summary statistics for the background strain # Recalculate summary statistics for the background strain
message("Calculating summary statistics for background strain") message("Calculating summary statistics for background strain")
list(summary_stats_bg, df_bg_stats) <- ss <- calculate_summary_stats(df_bg, variables, group_vars = c("OrfRep", "conc_num", "conc_num_factor"))
calculate_summary_stats(df_bg, variables, group_vars = c("OrfRep", "conc_num", "conc_num_factor")) summary_stats_bg <- ss$summary_stats
df_bg_stats <- ss$df_with_stats
write.csv(summary_stats_bg, write.csv(summary_stats_bg,
file = file.path(out_dir, paste0("SummaryStats_BackgroundStrains_", strain, ".csv")), file = file.path(out_dir, paste0("SummaryStats_BackgroundStrains_", strain, ".csv")),
row.names = FALSE) row.names = FALSE)