import.counts.data {SparseSignatures} | R Documentation |
Import point mutations data to build the count matrix to extract mutatational signatues.
import.counts.data(input, bsg, mutation_categories)
input |
either a data.frame/data.table object or a file with 5 columns: sample name, chromosome, position, ref, alt. |
bsg |
a BSgenome object for the reference genome. Chromosome names have to match the input table. |
mutation_categories |
array with the 96 mutational categories to be considered. It is provided along with the package by data(mutation_categories). |
A count matrix to extract mutatational signatues
data(ssm560_reduced) library("BSgenome.Hsapiens.1000genomes.hs37d5") bsg = BSgenome.Hsapiens.1000genomes.hs37d5 data(mutation_categories) imported_data = import.counts.data(input=ssm560_reduced,bsg=bsg,mutation_categories=mutation_categories)