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

In campbio/BAGEL: Novel Mutational Signature Analysis

Description

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

Usage

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

Arguments

bay	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 bagel

Examples

#bay <- readRDS(system.file("testdata", "bagel_sbs96_tiny.rds",
#package = "BAGEL"))
#add_flank_to_variants(bay, 1, 2)
#add_flank_to_variants(bay, -2, -1)

campbio/BAGEL documentation built on Oct. 6, 2020, 3:59 a.m.