eventOutcomeCompare: eventOutcomeCompare

In SPLINTER: Splice Interpreter of Transcripts

Description

Compares two sequences and gives differences if there's a switch from 1->2 if seq2 is NULL, assume seq1 is a list of length 2 to compare

Usage

eventOutcomeCompare(
  seq1,
  seq2 = NULL,
  genome,
  direction = TRUE,
  fullseq = TRUE,
  verbose = FALSE
)

Arguments

seq1	GRangesList
seq2	GRangesList
genome	BSGenome object
direction	logical. Report direction of sequence change.
fullseq	logical. Report full sequences.
verbose	logical. turn messages on/off.

Value

list containing
(1) tt : PairwiseAlignmentsSingleSubject pairwise alignment
(2) eventtypes : string detailing primary event classification

Author(s)

Diana LOW

Examples

suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
bsgenome<-BSgenome.Mmusculus.UCSC.mm9
eventOutcomeCompare(seq1=compatible_cds$hits[[1]],seq2=region_minus_exon,
 genome=bsgenome,direction=TRUE)

SPLINTER documentation built on Nov. 8, 2020, 8:13 p.m.