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utr.annotation (version 1.0.4)

getTranscriptIdsForUTRVariants: Find the ensembl_transcript_id for utr variants genes, or cds

Description

getTranscriptIdsForUTRVariants find transcripts if a variant fall in their specified region and return all transcripts id for each variant in the variant table

Usage

getTranscriptIdsForUTRVariants(variantsTable, transcriptRegions, checkRegion)

Arguments

variantsTable

variants table

transcriptRegions

transcripts structure table from Ensembl

checkRegion

check if a transcript within a region: utr5 or utr3 or cds

Value

A list containing ensembl_transcript_id of each variant which its mutation Pos is within those transcripts checkRegion.