utr.annotation (version 1.0.4)

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

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