getTSSKozakOneVariant: Get the Kozak sequence in TSS region for transcripts in...

In utr.annotation: Annotate Variants in the Untranslated Regions

Description

Get the Kozak sequence in TSS region for transcripts in transcriptIdColumn for one variant.

Usage

getTSSKozakOneVariant(
  variant,
  utr5SeqTable,
  codingSeqTable,
  transcriptIdColumn
)

Arguments

utr5SeqTable	5' UTR sequence table from Ensembl DB. Have two columns: ensembl_transcript_id and seq
codingSeqTable	coding sequence table from Ensembl DB. Have two columns: ensembl_transcript_id and seq
transcriptIdColumn	the name of the transcript id column for the codon region
variantsTable	variants table

Value

A string concatenated TSS Kozak sequences (NA if the transcript id in that row is NA)

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