Extracts the trinucleotide context for a set of mutations

Extracts the trinucleotide context for a set of mutations

extract_trinucleotide_context(mutations, reference, destrand = TRUE)

Arguments

mutations	A data frame having the mutations. Should have the columns CHROM, POS, REF, ALT.
reference	the reference genome in BSgenome format
destrand	logical, whether to destrand mutations

Value

A data frame with two columns having the substitutions and the trinucleotide context

Examples

# \donttest{
data("mutations", package = "ctDNAtools")
## Use human reference genome from BSgenome.Hsapiens.UCSC.hg19 library
suppressMessages(library(BSgenome.Hsapiens.UCSC.hg19))

## with destranding
extract_trinucleotide_context(mutations, BSgenome.Hsapiens.UCSC.hg19)
#>    substitution context
#> 1            CG     A_A
#> 2            CA     G_T
#> 3            TA     A_T
#> 4            TC     T_A
#> 5            TA     A_G
#> 6            CA     G_A
#> 7            TG     G_T
#> 8            TG     T_T
#> 9            TC     T_A
#> 10           CT     T_T

## without destranding
extract_trinucleotide_context(mutations, BSgenome.Hsapiens.UCSC.hg19,
  destrand = FALSE
)
#>    substitution context
#> 1            CG     A_A
#> 2            GT     A_C
#> 3            AT     A_T
#> 4            TC     T_A
#> 5            TA     A_G
#> 6            CA     G_A
#> 7            AC     A_C
#> 8            AC     A_A
#> 9            AG     T_A
#> 10           CT     T_T
# }