mut.info: Get the information of mutated sequence

Description Usage Arguments Details Value Examples

Description

mut.info returns the sequences and positional infomation of a mutated gene.

Usage

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mut.info(gene_id, ref, 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

Returns the sequences and positional infomation of a mutated gene.

Value

charactor vector containing five entries:

Examples

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library(masonmd)
# an example of NMD-escape mutation from TCGA
mut.info(gene_id = 13, ref = 37, mut_start = 151545640, mut_end = 151545640,
ref_nt = "G",mut_nt = "T")

ZYBunnyHu/masonmd documentation built on May 10, 2019, 1:55 a.m.