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

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

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:

• 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 = "+")

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