parseMatsGeneric {psichomics}R Documentation

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

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:

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 intron retention 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 = "+")

[Package psichomics version 1.12.1 Index]