samples {FRASER} | R Documentation

## Getter/Setter methods for the FraserDataSet The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object. `samples` sets or gets the sample IDs; `condition` ; `nonSplicedReads` return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds.

### Description

Getter/Setter methods for the FraserDataSet

The following methods are getter and setter methods to extract or set certain values of a FraserDataSet object.

`samples` sets or gets the sample IDs; `condition` ; `nonSplicedReads` return a RangedSummarizedExperiment object containing the counts for the non spliced reads overlapping splice sites in the fds.

Mapping of chromosome names

### Usage

    samples(object)

    samples(object) <- value

    condition(object)

    condition(object) <- value

    bamFile(object)

    bamFile(object) <- value

    name(object)

    name(object) <- value

    strandSpecific(object)

    strandSpecific(object) <- value

    pairedEnd(object)

    pairedEnd(object) <- value

    workingDir(object)

    workingDir(object) <- value

    scanBamParam(object)

    scanBamParam(object) <- value

    nonSplicedReads(object)

    nonSplicedReads(object) <- value

    ## S4 method for signature 'FraserDataSet'
    samples(object)

    ## S4 replacement method for signature 'FraserDataSet'
    samples(object) <- value

    ## S4 method for signature 'FraserDataSet'
    condition(object)

    ## S4 replacement method for signature 'FraserDataSet'
    condition(object) <- value

    ## S4 method for signature 'FraserDataSet'
    bamFile(object)

    ## S4 replacement method for signature 'FraserDataSet'
    bamFile(object) <- value

    ## S4 method for signature 'FraserDataSet'
    name(object)

    ## S4 replacement method for signature 'FraserDataSet'
    name(object) <- value

    ## S4 method for signature 'FraserDataSet'
    workingDir(object)

    ## S4 replacement method for signature 'FraserDataSet'
    workingDir(object) <- value

    ## S4 method for signature 'FraserDataSet'
    strandSpecific(object)

    ## S4 replacement method for signature 'FraserDataSet'
    strandSpecific(object) <- value

    ## S4 method for signature 'FraserDataSet'
    pairedEnd(object)

    ## S4 replacement method for signature 'FraserDataSet'
    pairedEnd(object) <- value

    ## S4 method for signature 'FraserDataSet'
    scanBamParam(object)

    ## S4 replacement method for signature 'FraserDataSet'
    scanBamParam(object) <- value

    ## S4 method for signature 'FraserDataSet'
    nonSplicedReads(object)

    ## S4 replacement method for signature 'FraserDataSet'
    nonSplicedReads(object) <- value

    FRASER.mcols.get(x, type = NULL, ...)

    FRASER.rowRanges.get(x, type = NULL, ...)

    mapSeqlevels(fds, style = "UCSC", ...)

### Arguments

`object` | A FraserDataSet object.
`value` | The new value that should replace the current one.
`x` | A FraserDataSet object.
`type` | The psi type (psi3, psi5 or theta)
`...` | Further parameters. For mapSeqLevels: further parameters passed to GenomeInfoDb::mapSeqlevels().
`fds` | FraserDataSet
`style` | The style of the chromosome names.

### Value

Getter method return the respective current value.

### Author(s)

Christian Mertes mertes@in.tum.de

Ines Scheller scheller@in.tum.de

### Examples

    fds <- createTestFraserDataSet()
    samples(fds)
    samples(fds) <- 1:dim(fds)[2]
    condition(fds)
    condition(fds) <- 1:dim(fds)[2]
    bamFile(fds) # file.paths or objects of class BamFile
    bamFile(fds) <- file.path("bamfiles", samples(fds), "rna-seq.bam")
    name(fds)
    name(fds) <- "My Analysis"
    workingDir(fds)
    workingDir(fds) <- tempdir()
    strandSpecific(fds)
    strandSpecific(fds) <- TRUE
    strandSpecific(fds) <- "reverse"
    strandSpecific(fds)
    scanBamParam(fds)
    scanBamParam(fds) <- ScanBamParam(mapqFilter=30)
    nonSplicedReads(fds)
    rowRanges(fds)
    rowRanges(fds, type="theta")
    mcols(fds, type="psi5")
    mcols(fds, type="theta")
    seqlevels(fds)
    seqlevels(mapSeqlevels(fds, style="UCSC"))
    seqlevels(mapSeqlevels(fds, style="Ensembl"))
    seqlevels(mapSeqlevels(fds, style="dbSNP"))

[Package FRASER version 1.4.0 Index]