add_flank_to_variants: Uses a genome object to find context and add it to the...

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Uses a genome object to find context and add it to the variant table

Description

Uses a genome object to find context and add it to the variant table

Usage

add_flank_to_variants(
  musica,
  g,
  flank_start,
  flank_end,
  build_table = TRUE,
  overwrite = FALSE
)

Arguments

musica	Input samples
g	A BSgenome object indicating which genome reference the variants and their coordinates were derived from.
flank_start	Start of flank area to add, can be positive or negative
flank_end	End of flank area to add, can be positive or negative
build_table	Automatically build a table using the annotation and add
overwrite	Overwrite existing count table

Value

None it to the musica

Examples

data(musica_sbs96_tiny)
g <- select_genome("19")
add_flank_to_variants(musica_sbs96_tiny, g, 1, 2)
add_flank_to_variants(musica_sbs96_tiny, g, -2, -1)

campbio/musicatk documentation built on July 14, 2024, 8:28 a.m.