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utr.annotation (version 1.0.4)

getCodon: Get the codon sequence for transcripts in transcriptIdColumn.

Description

getCodon Get the codon sequence for transcripts in transcriptIdColumn.

Usage

getCodon(variantsTable, seqTable, transcriptIdColumn, codonRegion)

Arguments

variantsTable

variants table

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 list containing codon sequences (NA if the transcript id in that row is NA). If transcriptIdColumn does not exist in the variantsTable, return NA