get_mut_seq_exjun: Get mutated coding sequence and junctions

Description Usage Arguments Details Value

View source: R/masonmd.R

Description

Get mutated coding sequence and junctions

Usage

1
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get_mut_seq_exjun(wt_exjun, wt_seq, mut_start, mut_end, mut_nt, ref_nt, note,
  txid)

Arguments

wt_exjun

a string that consists of 0 or 1 to indicates the positions of exon-exon junctions in the coding sequence;

wt_seq

wildtype coding sequence

mut_start

position of mutation start in chromosome

mut_end

position of mutation end in chromosome

mut_nt

nucleotides after alteration

ref_nt

the nucleotides on the reference genome at the mutated position; the nucleotides before mutation

note

extra notes

txid

transcript ID

Details

Get the mutated sequence and junctions

Value

A list containing three entries:


zhiyuanhu/masonmd documentation built on May 3, 2018, 10:23 p.m.