annotate_isomut: Annotate isomut data

In fridoling/isomutR: isomutR

Description

annotate_isomut adds information about the location of variants (coding or intergenic) and, for coding variants, about the affected gene(s) and the position of the variant in the gene.

Usage

annotate_isomut(
  isomut,
  ref = system.file("extdata", "Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa",
    package = "isomutR"),
  annotation = gtf_scer,
  txdb = NULL,
  noDups = FALSE,
  predictCoding = TRUE,
  ...
)

Arguments

isomut	a data.frame of isomut data as generated by read_isomut (minimally needs to contain chr and pos columns.
annotation	path to annotation file in gtf or gff format or GRanges object containing the annotations.
txdb	optionally provide TxDb object (should match anno).
noDups	don't keep multiple annotations (e.g. when variant is inside two genes on opposite strands). Default FALSE.
predictCoding	predict consequences of variants in coding regions.
...	further arguments for predict_coding.

Value

a data.frame with additional columns regarding annotation.

fridoling/isomutR documentation built on Jan. 21, 2022, 4:45 a.m.