parseSuppaGeneric: Parse junctions of an event from SUPPA

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

Parse junctions of an event from SUPPA

Description

Parse junctions of an event from SUPPA

Usage

parseSuppaGeneric(junctions, strand, coords, plus_pos, minus_pos)

parseSuppaSE(junctions, strand)

parseSuppaRI(junctions, strand)

parseSuppaALE(junctions, strand)

parseSuppaAFE(junctions, strand)

parseSuppaMXE(junctions, strand)

parseSuppaA3SS(junctions, strand)

parseSuppaA5SS(junctions, strand)

Arguments

junctions	List of integers: exon-exon junctions of an event
strand	Character: positive-sense (+) or negative-sense (-) strand
coords	Character: coordinate positions to fill
plus_pos	Integer: index of the coordinates for a plus strand event
minus_pos	Integer: index of the coordinates for a minus strand event

Details

The following event types are available to be parsed:

• SE (exon skipping)

• RI (retained intron)

• MXE (mutually exclusive exons)

• A5SS (alternative 5' splice site)

• A3SS (alternative 3' splice site)

• ALE (alternative last exon)

• AFE (alternative first exon)

Value

Data frame of parsed junctions

See Also

parseSuppaEvent()

Examples

# Parse generic event (in this case, an exon skipping event)
junctions <- read.table(text = "169768099 169770024 169770112 169771762")
coords <- c("C1.end", "A1.start", "A1.end", "C2.start")
plus  <- 1:4
minus <- 1:4
psichomics:::parseSuppaGeneric(junctions, strand = "+", coords, plus, minus)

junctions <- read.table(text = "169768099 169770024 169770112 169771762")
psichomics:::parseSuppaSE(junctions, "+")

junctions <- read.table(text = "196709749 196709922 196711005 196711181")
psichomics:::parseSuppaRI(junctions, "+")

junctions <- read.table(
    text = "24790610 24792494 24792800 24790610 24795476 24795797")
psichomics:::parseSuppaALE(junctions, "+")

junctions <- read.table(
    text = "169763871 169764046 169767998 169764550 169765124 169767998")
psichomics:::parseSuppaAFE(junctions, "+")

junctions <- read.table(
    text = "202060671 202068453 202068489 202073793 202060671 202072798 202072906 202073793")
psichomics:::parseSuppaMXE(junctions, "+")

junctions <- read.table(text = "169772450 169773216 169772450 169773253")
psichomics:::parseSuppaA3SS(junctions, "+")

junctions <- read.table(text = "50193276 50197008 50192997 50197008")
psichomics:::parseSuppaA5SS(junctions, "+")

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