Driver analysis

library(ithi.utils)
load_base_libs()

library(ithi.meta)
library(ithi.seq)

Colour palettes

pal_patient <- select_palette("patient")
pal_effect <- select_palette("effect")

Parameters

db_path <- snakemake@params$db

driver_file <- snakemake@input$driver_file
gene_list <- snakemake@input$gene_list_file

Metadata

db <- src_sqlite(db_path, create = FALSE)
samples <- collect(tbl(db, "samples"))
wgss <- collect(tbl(db, "wgs"))

Calls

drivers <- fread(driver_file)
gene_list <- fread(gene_list)

drivers_filtered <- filter_drivers(drivers, gene_list, method = "first")

Somatic variants

CNV calls are made with Remixt, SNV calls are (at the moment) from Strelka.

drivers_processed <- process_driver_info(drivers_filtered, subselect = TRUE)

samples_merged <- plyr::join(samples, wgss, type = "inner")
sample_list <- subset(samples_merged, project_code == "ITH" & !source %in% c("normal", 
    "blood") & patient_id != "8")$condensed_id

driver_oncoplot(drivers_processed, sample_list, pal_patient, pal_effect)

BRCA1 

BRCA2 

CCNE1 

CDKN2A 

KRAS 

MECOM 

MYC 

NF1 

PTEN 

RB1 

TP53 

Must add custom legend.