inst/scripts/Format_signatures.R

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

#Script to convert a signature file from SIGNAL into the correct format for MutationalPatterns
library(dplyr)
library(stringr)
library(readr)
library(magrittr)

format_SIGNAL_signatures = function(fname){
    signatures =read.table(fname, 
                           header = TRUE, 
                           sep = "\t", 
                           stringsAsFactors = FALSE,
                           dec = ",")
    
    colnames(signatures)[1] = "Type_subtype"
    signatures = signatures %>% 
        dplyr::mutate(Type = str_replace(Type_subtype, ".*\\[(.*)\\].*", "\\1"),
                      SubType = str_remove_all(Type_subtype, "\\[|\\]|\\>[A-Z]")) %>% 
        dplyr::select(-Type_subtype) %>% 
        dplyr::select(Type, SubType, everything())
    
    fname_base = basename(fname)
    out_path = file.path("inst", "extdata", "signatures", fname_base)
    write.table(signatures, 
                out_path, 
                sep = "\t",
                row.names = FALSE,
                quote = FALSE)
    invisible(0)
}

format_SIGNAL_signatures("~/Downloads/snv_SIGNAL_tissue.txt")
format_SIGNAL_signatures("~/Downloads/snv_SIGNAL_reference.txt")
format_SIGNAL_signatures("~/Downloads/snv_SIGNAL_exposure.txt")

#DBS data was not on signature website, but has been extracted from the paper:
# "A Compendium of Mutational Signatures of Environmental Agents

#Add sparse signatures from the paper:
# "De Novo Mutational Signature Discovery in Tumor Genomes using SparseSignatures"
signatures = read_tsv("~/Downloads/snv_SPARSE.txt", 
                      col_types = cols(.default = "d", sig = "c"), 
                      locale=locale(decimal_mark = ","))
signatures = signatures %>% 
    tidyr::pivot_longer(-sig, names_to = "Type_subtype", values_to = "values") %>% 
    tidyr::pivot_wider(names_from = sig, values_from = values) %>% 
    dplyr::mutate(Type = str_replace(Type_subtype, ".*\\[(.*)\\].*", "\\1"),
                  SubType = str_remove_all(Type_subtype, "\\[|\\]|\\>[A-Z]")) %>% 
    dplyr::select(-Type_subtype) %>% 
    dplyr::select(Type, SubType, everything())

write.table(signatures, 
            "inst/extdata/signatures/snv_SPARSE_reference.txt", 
            sep = "\t",
            row.names = FALSE,
            quote = FALSE)


#Format COSMIC snv signatures
format_COSMIC_signatures = function(in_fname, extra_sigs, out_fname, muttype){
    
    #Read main signature file
    signatures = read.table(in_fname,
               sep = ",",
               stringsAsFactors = FALSE,
               header = TRUE)
    
    if (!.is_na(extra_sigs)){
        #Read separate signature files
        sig_fnames = paste0("~/Downloads/sigProfiler_",
                            muttype, 
                            "_signatures_", 
                            extra_sigs, 
                            ".csv")
        sigs_to_add_m = purrr::map(sig_fnames, ~read.table(.x, 
                                                           sep = ",", 
                                                           stringsAsFactors = FALSE, 
                                                           header = TRUE)) %>% 
            purrr::map(function(x) x[, ncol(x), drop = FALSE]) %>% 
            do.call(cbind, .)
        
        #Fix column names
        colnames(sigs_to_add_m) = str_remove(colnames(sigs_to_add_m), "_GRCh37")
        
        #Combine in one single data.frame.
        signatures = cbind(signatures, sigs_to_add_m)
    }
    #Write out
    out_path = file.path("inst", "extdata", "signatures", out_fname)
    write.table(signatures, 
                out_path, 
                sep = "\t",
                row.names = FALSE,
                quote = FALSE)
    invisible(0)
}

format_COSMIC_signatures("~/Downloads/sigProfiler_ID_signatures.csv",
                         paste0("ID", c(18)),
                         "indel_COSMIC_reference.txt",
                         "ID")

format_COSMIC_signatures("~/Downloads/sigProfiler_DBS_signatures.csv",
                         NA,
                         "dbs_COSMIC_reference.txt",
                         NA)

format_COSMIC_signatures("~/Downloads/sigProfiler_TSB_signatures.csv",
                         NA,
                         "tsb_snv_COSMIC_reference.txt")


# Format Cosmic signatures for the SNVs
mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
                               package = "MutationalPatterns"
))

# Read in Cosmic signatures 3.1
sbs_sigs = read.table("~/Downloads/cosmic_v3.1.txt", dec = ",", header = T) %>% 
    dplyr::mutate(cont = paste0(str_sub(Subtype, 1, 1), "[", Type, "]", str_sub(Subtype, 3))) %>% 
    dplyr::mutate(cont = factor(cont, levels = rownames(mut_mat))) %>% 
    dplyr::arrange(cont) %>% 
    dplyr::select(-cont)


sbs_sigs = as.matrix(sbs_sigs[,-c(1,2)])
write.table(sbs_sigs, 
            "~/surfdrive/Shared/Boxtel_General/Scripts/Git_submission/Freek_MutationalPatterns/MutationalPatterns/inst/extdata/signatures/snv_COSMIC_reference.txt",
            quote = F, row.names = F, sep = "\t")