TargetExperiment-getters: Getters for TargetExperiment and TargetExperimentList...

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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 [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

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")

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.