parseVastToolsSE {psichomics} | R Documentation |
Parse junctions of an event from VAST-TOOLS according to event type
parseVastToolsSE(junctions) parseVastToolsRI(junctions, strand) parseVastToolsA3SS(junctions) parseVastToolsA5SS(junctions)
junctions |
Data.frame or matrix: exon-exon junctions of alternative splicing events (it must have 4 columns) |
strand |
Character: positive (+) or negative (-) strand |
The following event types are available to be parsed:
SE (skipped exon)
RI (retained intron)
A5SS (alternative 5' splice site)
A3SS (alternative 3' splice site)
List of parsed junctions
junctions <- read.table(text = "41040823 41046768 41046903 41051785") psichomics:::parseVastToolsSE(junctions) # these functions are vectorised! junctions <- read.table(text = "41040823 41046768 41046903 41051785 58864658 58864693 58864294 58864563") psichomics:::parseVastToolsSE(junctions) junctions <- read.table(text = "58864658 58864693 58864294 58864563") psichomics:::parseVastToolsRI(junctions, strand = "+") junctions <- rbind( c(36276385, list(c(36277798, 36277315)), 36277974), c(7133604, 7133377, list(c(7133474, 7133456))) ) psichomics:::parseVastToolsA3SS(junctions) junctions <- rbind( c(74650610, list(c(74650654, 74650658)), 74650982), c(list(c(49557666, 49557642), 49557746, 49557470)) ) psichomics:::parseVastToolsA5SS(junctions)