getBedFile {TarSeqQC} | R Documentation

## Getters for TargetExperiment and TargetExperimentList objects.

### Description

Obtain information about TargetExperiment and TargetExperimentList slots, according to the given function call.

### Usage

    getBedFile(object)

    ## S4 method for signature 'TargetExperiment'
    getBedFile(object)

    getBamFile(object)

    ## S4 method for signature 'TargetExperiment'
    getBamFile(object)

    getFastaFile(object)

    ## S4 method for signature 'TargetExperiment'
    getFastaFile(object)

    getFeaturePanel(object)

    ## S4 method for signature 'TargetExperiment'
    getFeaturePanel(object)

    getGenePanel(object)

    ## S4 method for signature 'TargetExperiment'
    getGenePanel(object)

    getFeature(object)

    ## S4 method for signature 'TargetExperiment'
    getFeature(object)

    getAttribute(object)

    ## S4 method for signature 'TargetExperiment'
    getAttribute(object)

    getScanBamP(object)

    ## S4 method for signature 'TargetExperiment'
    getScanBamP(object)

    getPileupP(object)

    ## S4 method for signature 'TargetExperiment'
    getPileupP(object)

    getRegion(object, level, ID, collapse = TRUE)

    ## S4 method for signature 'TargetExperiment'
    getRegion(object, level, ID, collapse = TRUE)

    getLowCtsFeatures(object, level, threshold = 50)

    ## S4 method for signature 'TargetExperiment'
    getLowCtsFeatures(object, level, threshold = 50)

    getOverlappedRegions(object, collapse = FALSE)

    ## S4 method for signature 'TargetExperiment'
    getOverlappedRegions(object, collapse = FALSE)

    ## S4 method for signature 'TargetExperimentList'
    getBedFile(object)

    getPanels(object)

    ## S4 method for signature 'TargetExperimentList'
    getPanels(object)

    ## S4 method for signature 'TargetExperimentList'
    getFeature(object)

    ## S4 method for signature 'TargetExperimentList'
    getAttribute(object)

    ## S4 method for signature 'TargetExperimentList'
    getRegion(object, level, ID, collapse = TRUE)

    ## S4 method for signature 'TargetExperimentList'
    getLowCtsFeatures(object, level,
        threshold = 50)

### Arguments

`object` | TargetExperiment/TargetExperimentList class object.
`level` | Character indicating 'gene' or 'feature'. Useful to getRegion function
`ID` | Character indicating the feature name that getRegion should be found.
`collapse` | Logical. Should the region be collapsed?.
`threshold` | Numeric what should be the minimum attribute value?.

### Value

according to the call one of the following objects can be returned

`GRanges` | bed file of the experiment
`BamFile` | reference to the BAM file
`FaFile` | reference to the fasta file
`GRanges` | feature panel with statistical information
`GRanges` | summarized version of the feature panel at gene level
`character` | name of the explored features (e.g 'amplicon', 'exon')
`character` | name of the analyzed attribute ('coverage' or 'medianCounts')
`ScanBamParam` | parameters for the scan of the BAM file
`PileupParam` | parameters for the pileup building
`data.frame` | regions or low counts features
`data.frame` | regions definition for overlapped features
`GRanges` | feature panels with statistical information

### Note

see full example in `TargetExperiment-class`

### Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

### See Also

`TargetExperiment-class`

### Examples

    ## Loading the TargetExperiment object
    data(ampliPanel,package="TarSeqQC")
    ## Get the bedFile slot
    getBedFile(ampliPanel)
    ## Get the bamFile slot
    getBamFile(ampliPanel)
    ## Get the fastaFile slot
    getFastaFile(ampliPanel)
    ## Get the feateurePanel slot
    getFeaturePanel(ampliPanel)
    ## Get the genePanel slot
    getGenePanel(ampliPanel)
    ## Get the Feature slot
    getFeature(ampliPanel)
    ## Get the attribute slot
    getAttribute(ampliPanel)
    ## Get the scanBamP slot
    getScanBamP(ampliPanel)
    ## Get the pileupP slot
    getPileupP(ampliPanel)
    ## Get the region related to a feature or a gene
    getRegion(ampliPanel, level="gene", ID="gene7", collapse=FALSE)
    ## Get the low counts features
    getLowCtsFeatures(ampliPanel, level="feature")
    ## Get the regions of overlapped features
    getOverlappedRegions(ampliPanel,collapse=FALSE)
    ## Loading the TargetExperimentList object
    data(TEList,package="TarSeqQC")
    ## Get the bedFile slot
    getBedFile(TEList)
    ## Get the panels slot
    getPanels(TEList)
    ## Get the Feature slot
    getFeature(TEList)
    ## Get the attribute slot
    getAttribute(TEList)
    ## Get the region related to a feature or a gene
    getRegion(TEList, level="gene", ID="gene7", collapse=FALSE)

    ## Get the low counts features
    getLowCtsFeatures(TEList, level="feature")

[Package TarSeqQC version 1.16.0 Index]