FraserDataSet: The FRASER dataset object

In c-mertes/FraseR: Find RAre Splicing Events in RNA-Seq Data

The FRASER dataset object

Description

Constructs an FRASER object based on the given input. It can take only the annotation (colData) or count tables (junctions/spliceSites).

Usage

FraserDataSet(colData = NULL, junctions = NULL, spliceSites = NULL, ...)

Arguments

colData	A DataFrame containing the annotation of the samples
junctions, spliceSites	A data.frame like object containing the raw counts for each junction or splice site. It requires the columns startID and endID for the junctions and spliceSiteID and type for the splice sites. Those columns identifies the corresponding splice site for the given junction and map to the splice site. For each sample the counts are saved in a corresponding column with the same name. It can also be a GRange object.
...	Any parameters corresponding to the slots and their possible values. See FraserDataSet

Value

A FraserDataSet object.

Author(s)

Christian Mertes [e-mail]

Examples

  fraser <- FraserDataSet()
  
  # example sample annoation
  sampleTable <- fread(system.file("extdata",
          "sampleTable_countTable.tsv", package="FRASER", mustWork=TRUE))
 
  # get raw counts 
  junctionCts   <- fread(system.file("extdata", 
          "raw_junction_counts.tsv.gz", package="FRASER", mustWork=TRUE))
  spliceSiteCts <- fread(system.file("extdata", 
          "raw_site_counts.tsv.gz", package="FRASER", mustWork=TRUE))
  
  # create FRASER object
  fds <- FraserDataSet(colData=sampleTable, junctions=junctionCts,
          spliceSites=spliceSiteCts, name="Example Dataset")
  

c-mertes/FraseR documentation built on June 15, 2024, 3:29 a.m.