getTranscriptIdsForOneCodonVariant: Find the ensembl_transcript_id and codon postions for one...

In utr.annotation: Annotate Variants in the Untranslated Regions

Description

Find the ensembl_transcript_id and codon postions for one variant

Usage

getTranscriptIdsForOneCodonVariant(
  variant,
  transcriptRegions,
  checkRegion,
  start,
  end
)

Arguments

variant	one row of variants table
transcriptRegions	transcripts structure table from ensembl
checkRegion	check if a transcript within a region stopCodon or startCodon
start	column name of the start region of checkRegion in transcripts structure table
end	column name of the end region of checkRegion in transcripts structure table

Details

For each variant, get all transcripts and extract their checkRegion's coordinates. For each transcript, check if the mutation Pos is within the region, if so, add that transcript's ensembl_transcript_id. If the mutation Pos is within multiple transcripts checkRegions, the transcripts ids are concatenate into one string with ";".

Value

A data table containing two columns: ensembl_transcript_id (id of transcripts for each variant which its mutation Pos is within those transcripts checkRegion.) codon_positions (positions of each nucleotides in the codon)

utr.annotation documentation built on Aug. 23, 2021, 9:06 a.m.