eventOutcomeCompare

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

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

Arguments

seq1

GRangesList

seq2

GRangesList

genome

BSGenome object

direction

logical. Report direction of sequence change.

fullseq

logical. Report full sequences.

Value

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

Author(s)

Diana LOW

Examples

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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)