src for ashm counts

scripts/count_ashm_freq.R

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+library(GAMBLR)
+library(tidyverse)
+
+setwd("/projects/rmorin/projects/gambl-repos/gambl-kdreval/")
+
+pathologies <- c("DLBCL", "FL", "CLL", "BL")
+
+
+g_metadata <- get_gambl_metadata() %>%
+    filter(pathology %in% pathologies)
+
+g_maf <- get_ssm_by_samples(
+    these_samples_metadata = g_metadata
+)
+
+annotated <- cool_overlaps(
+    g_maf,
+    grch37_ashm_regions %>%
+        mutate(
+            chr_name = gsub("chr", "", chr_name),
+            name = paste(gene, region, sep = "_")
+        ),
+    columns2 = c("chr_name", "hg19_start", "hg19_end")
+)
+
+colnames(annotated)
+mutated_counts <- annotated %>%
+    count(
+        gene, name, Tumor_Sample_Barcode
+    )
+
+pathology_counts <- g_metadata %>%
+    select(Tumor_Sample_Barcode, pathology) %>%
+    group_by(pathology) %>%
+    mutate(total = n()) %>%
+    ungroup
+
+all_counts <- left_join(
+    mutated_counts,
+    pathology_counts
+)
+
+all_counts <- all_counts %>%
+    group_by(pathology, name) %>%
+    mutate(mut = n()) %>%
+    ungroup %>%
+    select(-c(Tumor_Sample_Barcode, n)) %>%
+    distinct
+
+all_counts <- all_counts %>%
+    mutate(pc = round((mut/total)*100, 2)) %>%
+    pivot_wider(
+        names_from = pathology,
+        names_glue = "{pathology}_{.value}",
+        values_from = c(total, mut, pc)
+    ) %>% select(-gene)
+
+output <- left_join(
+    grch37_ashm_regions %>%
+        mutate(
+            name = paste(gene, region, sep = "_")
+        ) %>%
+        select(name, chr_name, hg19_start, hg19_end),
+    all_counts
+) %>%
+    replace_na(
+        list(
+            DLBCL_total = pull(unique(pathology_counts[pathology_counts$pathology=="DLBCL", "total"])),
+            FL_total = pull(unique(pathology_counts[pathology_counts$pathology=="FL", "total"])),
+            CLL_total = pull(unique(pathology_counts[pathology_counts$pathology=="CLL", "total"])),
+            BL_total = pull(unique(pathology_counts[pathology_counts$pathology=="BL", "total"]))
+        )
+    ) %>%
+    replace(is.na(.), 0)
+
+output <- output %>%
+    select(
+        name, chr_name, hg19_start, hg19_end,
+        contains("DLBCL"),
+        contains("FL"),
+        contains("CLL"),
+        contains("BL")
+    )
+
+write_tsv(
+    output,
+    "~/my_dir/repos/LLMPP/resources/curated/somatic_hypermutation_locations_with_DLBCL_frequencies.tsv"
+)