getBedFile {TarSeqQC} | R Documentation |
Obtain information about TargetExperiment and TargetExperimentList slots, according to the given function call.
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)
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?. |
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 |
see full example in TargetExperiment-class
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
## 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")