inst/scripts/create_example_dbs.R

In CuppenResearch/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

library(tidyverse)
library(VariantAnnotation)
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)

# Get grl
grl <- readRDS("inst/states/blood_grl.rds")

# Get dbs
grl_dbs <- get_mut_type(grl, "dbs")
saveRDS(grl_dbs, "inst/states/blood_grl_dbs.rds")

# Set context
grl_dbs_context <- get_dbs_context(grl_dbs)
saveRDS(grl_dbs_context, "inst/states/blood_grl_dbs_context.rds")

# Count contexts
dbs_counts <- count_dbs_contexts(grl_dbs_context)
saveRDS(dbs_counts, "inst/states/blood_dbs_counts.rds")

# Refit to signatures
signatures <- get_known_signatures("dbs")


fit_res <- fit_to_signatures(dbs_counts, signatures)
saveRDS(fit_res, "inst/states/dbs_refit.rds")