parseVastToolsSE: Parse junctions of an event from VAST-TOOLS according to...

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Parse junctions of an event from VAST-TOOLS according to event type

Description

Parse junctions of an event from VAST-TOOLS according to event type

Usage

parseVastToolsSE(junctions)

parseVastToolsRI(junctions, strand)

parseVastToolsA3SS(junctions)

parseVastToolsA5SS(junctions)

Arguments

junctions	Data.frame or matrix: exon-exon junctions of alternative splicing events (it must have 4 columns)
strand	Character: positive (+) or negative (-) strand

Details

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)

Value

List of parsed junctions

See Also

parseVastToolsEvent()

Examples

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)

nuno-agostinho/psichomics documentation built on Feb. 11, 2024, 11:16 p.m.