diff --git a/src/06_compute_tdd_index.R b/src/06_compute_tdd_index.R index 9aa3b48933459ba91348c8cf1e3ea5e2ae2c3a75..f86cef06736d95d85ddbb673a2cdbeb39e79c5e1 100644 --- a/src/06_compute_tdd_index.R +++ b/src/06_compute_tdd_index.R @@ -485,13 +485,18 @@ prepare_df_for_cor <- function(mean_gene_count = 10, ercc = F, clear = FALSE, # If TRUE, clears the bar when finish width = 100 ) # Width of the progress bar + ptotv <- NULL for (gn in genes) { pb$tick() tmp <- tdd_full %>% filter(gene == gn) fit <- lm(value ~ condition + time_point + replicate, data = tmp) p_val <- summary(fit)$coefficients["conditionDMSO_TDD", "Pr(>|t|)"] tdd_mean[tdd_mean$gene == gn, "p_value"] <- p_val + ptotv <- c(ptotv, p_val) } + padjs <- p.adjust(ptotv, method = "fdr") + tmp_table <- tibble(gene = genes, padj = padjs) + tdd_mean <- tdd_mean %>% left_join(tmp_table, by = "gene") tdd_full <- tdd_mean %>% arrange(-p_value) # nolint write_tsv(tdd_full, paste0(output_folder, "/full_TDD_correlation_table.txt")) dir <- "./data/gene_lists/" @@ -1064,6 +1069,7 @@ create_tdd_violin <- function(tp = 5, groupn = "up_down", ) my_range <- c(-0.5, 1) } else { + tdd_table <- tdd_table %>% filter(group != "CTRL") title <- paste0(title, " for genes up and down by BRAFi") tdd_table$group <- factor(tdd_table$group, level = c("BRAF_UP", "BRAF_DOWN")