1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
|
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")
|
