parseVastToolsEvent: Parses an alternative splicing event from VAST-TOOLS

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

Description

Parses an alternative splicing event from VAST-TOOLS

Usage

parseVastToolsEvent(event)

Arguments

event

Data.frame: VAST-TOOLS event containing gene symbol, event ID, length, junctions coordinates, event type and inclusion levels for both samples

Details

Junctions are parsed from

Value

List with the event attributes (chromosome, strand, event type and the position of the exon boundaries)

Note

Only supports to parse one event at a time.

Examples

event <- read.table(text = 
"NFYA HsaEX0042823 chr6:41046768-41046903 136 chr6:41040823,41046768-41046903,41051785 C2 0 N 0 N"
)
psichomics:::parseVastToolsEvent(event)

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'
     Program Gene.symbol     Event.ID Event.type Chromosome Inclusion.level.A
1 VAST-TOOLS        NFYA HsaEX0042823         SE       chr6                 0
  Inclusion.level.B C1.start   C1.end A1.start   A1.end A2.start A2.end
1                 0       NA 41040823 41046768 41046903       NA     NA
  C2.start C2.end Strand
1 41051785     NA      +

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