classify.nmd: Classify NMD-elicit mutations

Description Usage Arguments Details Value Examples

View source: R/masonmd.R

Description

classify.nmd can detect the premature stop codon (PTC) and predict NMD-elicit mutations based on three rules.

Usage

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classify.nmd(gene_id, ref = 37, mut_start, mut_end, ref_nt = "-",
  mut_nt = "-")

Arguments

gene_id

numeric; gene Entrez ID

ref

numeric; reference genome/NCBI build; ref = 37 if the mutation is called by build37/hg19, or ref = 36 if the mutation is called by build36/hg18

mut_start

numeric; the absolution start position of the mutations on chromosome on + strand

mut_end

numeric; the absolution end position of the mutations on chromosome on + strand

ref_nt

charactor; the reference nucleotides of the mutations on + strand; ref_nt = "-" for insertion

mut_nt

charactor; the mutation nucleotides on + strand; mut_nt = "-" for deletion

Details

classify the mutations into NMD or non-NMD, and return the position of premature stop codon in CDS

Value

A list containing eight entries:

Examples

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library(masonmd)
# an example of NMD-escape mutation from TCGA
classify.nmd(gene_id = 13, ref = 37, mut_start = 151545640, mut_end = 151545640,
ref_nt = "G",mut_nt = "T")
# an example of NMD-elicit mutation from TCGA
classify.nmd(gene_id = 2, ref = 37, mut_start = 9221429, mut_end = 9221429,
ref_nt = "G", mut_nt = "A")

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