parseMatsGeneric: Parse junctions of an alternative splicing event from MATS...

In psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

Description

Parse junctions of an alternative splicing event from MATS according to event type

Usage

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

parseMatsSE(junctions, strand)

parseMatsMXE(junctions, strand)

parseMatsRI(junctions, strand)

parseMatsA3SS(junctions, strand)

parseMatsA5SS(junctions, strand)

parseMatsAFE(junctions, strand)

parseMatsALE(junctions, strand)

Arguments

junctions	Integer: event's junctions
strand	Character: strand of the event
coords	Character: names of the alternative splicing coordinates
plus_pos	Integer: match of each junction in the respective coordinate for the plus strand
minus_pos	Integer: match of each junction in the respective coordinate for the minus strand

Details

The following event types are ready to be parsed:

• SE (skipped exon)

• MXE (mutually exclusive exon)

• RI (retained intron)

• A5SS (alternative 5' splice site)

• A3SS (alternative 3' splice site)

• AFE (alternative first exon)

• ALE (alternative last exon)

You can use parseMatsGeneric to parse other event types.

Value

Data frame with parsed junctions

See Also

parseMatsEvent()

Examples

# Parse generic event (in this case, an exon skipping event)
junctions <- read.table(text=
    "79685787 79685910 79685796 79685910 79679566 79679751")
coords <- c("A1.start", "A1.end",
            "C1.start", "C1.end",
            "C2.start", "C2.end")
plus  <- c(1:6)
minus <- c(2:1, 6:3)
psichomics:::parseMatsGeneric(junctions, strand = "+", coords, plus, minus)

# Parse exon skipping event
junctions <- read.table(text=
    "79685787 79685910 79685796 79685910 79679566 79679751")
psichomics:::parseMatsSE(junctions, strand = "+")

# Parse mutually exclusive exon event
junctions <- read.table(text=
"158282161 158282276 158282689 158282804 158281047 158281295 158283950 158284199")
psichomics:::parseMatsMXE(junctions, strand = "+")

# Parse retained intron event
junctions <- read.table(text=
    "15929853 15932100 15929853 15930016 15930687 15932100")
psichomics:::parseMatsRI(junctions, strand = "+")

# Parse alternative 3' splicing site event
junctions <- read.table(text=
    "79685787 79685910 79685796 79685910 79679566 79679751")
psichomics:::parseMatsA3SS(junctions, strand = "+")

# Parse alternative 5' splicing site event
junctions <- read.table(text=
    "102884421 102884501 102884421 102884489 102884812 102885881")
psichomics:::parseMatsA5SS(junctions, strand = "+")

# Parse alternative first exon event
junctions <- read.table(text=
    "16308723 16308879 16308967 16309119 16314269 16314426")
psichomics:::parseMatsAFE(junctions, strand = "+")

# Parse alternative last exon event
junctions <- read.table(text=
    "111858645 111858828 111851063 111851921 111850441 111850543")
psichomics:::parseMatsAFE(junctions, strand = "+")

psichomics documentation built on Nov. 8, 2020, 5:44 p.m.