produceSequenceFromHGVSCode: produceSequenceFromHGVSCode

In gdelangel/genomicRTools: Genomic R Tools

Description

Given an HGVS mutation code, produce corresponding cDNA and amino-acid sequence, starting from the ATG initiator codon and up to STOP codon. If mutation clobbers the STOP codon, sequence will be produced until cDNA string runs out.

Usage

produceSequenceFromHGVSCode(hgvs, transcriptID, wildTypeCDNA,
  lowerCaseChange = F, debug = F)

Arguments

hgvs	Character string with HGVS mutation code
transcriptID	Character string with ENST ID to which hgvs code corresponds
wildTypeCDNA	Character string with WT reference cDNA sequence
lowerCaseChange	Highlight change in lowercase
debug	Output debug info

Value

list with elements cdna and aa representing new cDNA and amino acid mutated sequence

Examples

str <- produceSequenceFromHGVSCode('c.571G>C','ENST00000374840',wtCDNA)

gdelangel/genomicRTools documentation built on May 16, 2019, 11:14 p.m.