testTXforStart: Test transcripts for annotated start codons

In fursham-h/ponder:

Description

This function will test whether the query transcript contain an annotated Start codon from a reference CCDS of the gene

Usage

testTXforStart(refCDS, queryTranscript, full.output = FALSE)

Arguments

queryTranscript	A GRanges object containing exon structure of a query transcript from the same gene family
refCDS	A GRanges object containing CCDS information of a gene family
full.output	If TRUE, function will output additional information

Value

By default, function will return a TRUE/FALSE boolean (annotatedStart)

If full.output is TRUE, function will output other information which include: (1) the length of the first coding exon (firstexlen), (2) queryTranscript GRanges with 5' end appended to the start codon (ORF), (3) a list of GRanges objects similar to 'indentifyAddedRemovedRegions()' output (txrevise_out). ?indentifyAddedRemovedRegions for more information

Author(s)

Fursham Hamid

Examples

testTXforStart(ptbp2Data$transcripts$ENSMUST00000197833, ptbp2Data$refCDS)
testTXforStart(ptbp2Data$afCDS, ptbp2Data$refCDS)

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