testNMD: Test ORF for NMD

In fursham-h/ponder:

Description

This function will test for NMD features of a transcript with a given open reading frame

Usage

testNMD(
  queryCDS,
  queryTranscript,
  distance_stop_EJ = 50,
  other_features = FALSE,
  fasta
)

Arguments

queryCDS	GRanges Object containing CDS structure of a transcript
queryTranscript	GRanges Object containing transcript structure of the same transcript
distance_stop_EJ	NMD Threshold. Distance of stop codon to last exon-exon junction. Default: 50
other_features	TRUE/FALSE argument to report other NMD features. Default: FALSE
fasta	Fasta sequence file. Mandatory if other_features == TRUE

Value

A list containing information on: (1) NMD nature of transcript (2) Distance of stop codon to last exon-exon junction if other features of NMD is to be returned: (3) coordinates of uORF (4) coordinates of uATG (5) frame of uATG

Author(s)

Fursham Hamid

Examples

library("BSgenome.Mmusculus.UCSC.mm10")
testNMD(ptbp2Data$refCDS, ptbp2Data$transcripts$ENSMUST00000029780)
testNMD(ptbp2Data$refCDS, ptbp2Data$transcripts$ENSMUST00000029780, other_features = TRUE, fasta = BSgenome.Mmusculus.UCSC.mm10)

testNMD(ptbp2Data$skipE10CDS, ptbp2Data$transcripts$ENSMUST00000197833)
testNMD(ptbp2Data$skipE10CDS, ptbp2Data$transcripts$ENSMUST00000197833, other_features = TRUE, fasta = BSgenome.Mmusculus.UCSC.mm10)

fursham-h/ponder documentation built on Dec. 27, 2019, 12:15 a.m.