Create Single Base Substitutions (SBS) counts matrix from input data for a provided reference genome.
getSBSCounts(data, reference = NULL)
Arguments
- 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.
Value
A matrix with Single Base Substitutions (SBS) counts per patient.
Examples
library('BSgenome.Hsapiens.1000genomes.hs37d5')
data(ssm560_reduced)
res <- getSBSCounts(data = ssm560_reduced, reference = BSgenome.Hsapiens.1000genomes.hs37d5)