eventOutcomeCompare {SPLINTER} | R Documentation |
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
eventOutcomeCompare(seq1, seq2 = NULL, genome, direction = TRUE, fullseq = TRUE)
seq1 |
GRangesList |
seq2 |
GRangesList |
genome |
BSGenome object |
direction |
logical. Report direction of sequence change. |
fullseq |
logical. Report full sequences. |
list containing
(1) tt : PairwiseAlignmentsSingleSubject pairwise alignment
(2) eventtypes : string detailing primary event classification
Diana LOW
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)