parseSuppaGeneric: Parse junctions of an event from SUPPA

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

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, "+")

Example output

Loading required package: shiny
Loading required package: shinyBS
Start the visual interface by running the function psichomics()
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
  C1.start    C1.end  A1.start    A1.end A2.start A2.end  C2.start C2.end
1       NA 169768099 169770024 169770112       NA     NA 169771762     NA
  C1.start    C1.end  A1.start    A1.end A2.start A2.end  C2.start C2.end
1       NA 169768099 169770024 169770112       NA     NA 169771762     NA
   C1.start    C1.end A1.start A1.end A2.start A2.end  C2.start    C2.end
1 196709749 196709922       NA     NA       NA     NA 196711005 196711181
  C1.start   C1.end A1.start   A1.end A2.start A2.end C2.start   C2.end
1       NA 24790610 24792494 24792800       NA     NA 24795476 24795797
   C1.start    C1.end  A1.start    A1.end A2.start A2.end  C2.start C2.end
1 169764550 169765124 169763871 169764046       NA     NA 169767998     NA
  C1.start    C1.end  A1.start    A1.end  A2.start    A2.end  C2.start C2.end
1       NA 202060671 202068453 202068489 202072798 202072906 202073793     NA
  C1.start    C1.end  A1.start A1.end A2.start A2.end  C2.start C2.end
1       NA 169772450 169773216     NA       NA     NA 169773253     NA
  C1.start   C1.end A1.start   A1.end A2.start A2.end C2.start C2.end
1       NA 50192997       NA 50193276       NA     NA 50197008     NA

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