predict_coding: Predict coding from variants

In fridoling/isomutR: isomutR

Description

predicts the consequences of variants in coding regions.

Usage

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

Arguments

isomut	a data.frame of isomut data as generated by read_isomut.
ref	either the name of a fasta file containing the reference genome or an object of class FaFile.
annotation	path to annotation file in gtf or gff format or GRanges object containing the annotations.
txdb	optionally provide TxDb object (should match annotation).
format_indels	whether indels should be formatted (see format_indels for details).
correct_coding	whether coding be corrected if two variants hit the same codon.
...	further arguments for correct_coding.

Value

a data.frame with additional columns regarding coding consequences.

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