predictMRLInAlt: Get the mutated 100nt 5' UTR sequence upstream of start codon...

In utr.annotation: Annotate Variants in the Untranslated Regions

Description

predictMRL Get the 100nt 5' UTR sequence upstream of start codon for transcripts in transcriptIdColumn and predict their MRL

Usage

predictMRLInAlt(variantsTable, seqTable, transcriptsTable, transcriptIdColumn)

Arguments

variantsTable	variants table
seqTable	corresponding 5' UTR sequence table from Ensembl DB. Have two columns: ensembl_transcript_id and seq
transcriptsTable	transcripts structure table from ensembl with start and end columns for start and end coordinates of the 5' UTR
transcriptIdColumn	the name of the transcript id column

Value

A list predicted MRL (NA if the transcript id in that row is NA). If transcriptIdColumn does not exist in the variantsTable, return NA

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