FraserDataSet {FRASER} | R Documentation

## 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 mertes@in.tum.de

### 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")

[Package FRASER version 1.4.0 Index]