utr.annotation (version 1.0.4)

getCodonOneVariant: Get the codon sequence of transcripts in transcriptIdColumn for one variant.

Description

getCodonOneVariant Get the codon sequence of transcripts in transcriptIdColumn for one variant.

Usage

getCodonOneVariant(variant, seqTable, transcriptIdColumn, codonRegion)

Arguments

variant

variant info

seqTable

cooresponding sequence table from Ensembl DB (either 5' UTR sequence or 3' UTR sequence). Have two columns: ensembl_transcript_id and seq

transcriptIdColumn

the name of the transcript id column for the codon region

codonRegion

"startCodon" or "stopCodon"

Value

A string concatenated codon sequences (NA if the transcript id in that row is NA) for one variant.