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 1.12.0 Index]