import.trinucleotides.counts {SparseSignatures} | R Documentation |
Make trinucleotides counts matrix from input data for a given reference genome.
import.trinucleotides.counts(data, reference = NULL)
data |
a data.frame with variants having 6 columns: sample name, chromosome, start position, end position, ref, alt. |
reference |
a BSgenome object with the reference genome to be used to retrieve flanking bases. |
A matrix with trinucleotides counts per patient.
data(ssm560_reduced) library("BSgenome.Hsapiens.1000genomes.hs37d5") trinucleotides_counts = import.trinucleotides.counts(data=ssm560_reduced, reference=BSgenome.Hsapiens.1000genomes.hs37d5)