GeneBreak-package | GeneBreak: A package for gene breakpoint detection on copy number abberation data |
accessOptions | Access Object Data. This method lists possible functions to access the data of the object. |
accessOptions-method | Access Object Data. This method lists possible functions to access the data of the object. |
addGeneAnnotation | addGeneAnnotation |
addGeneAnnotation-method | addGeneAnnotation |
bpFilter | bpFilter |
bpFilter-method | bpFilter |
bpGenes | bpGenes |
bpGenes-method | bpGenes |
bpPlot | bpPlot |
bpPlot-method | bpPlot |
bpStats | bpStats |
bpStats-method | bpStats |
breakpointData | Access Object breakpointData. This method returns a dataframe with breakpoint values per feature. |
breakpointData-method | Access Object breakpointData. This method returns a dataframe with breakpoint values per feature. |
breakpointsPerGene | Access Object breakpointsPerGene. This method returns a dataframe with breakpoints per gene. |
breakpointsPerGene-method | Access Object breakpointsPerGene. This method returns a dataframe with breakpoints per gene. |
callData | Access Object callData. This method returns a dataframe with feature call values. |
callData-method | Access Object callData. This method returns a dataframe with feature call values. |
copynumber.data.chr18 | CGHcall Example copynumber data hg18 chr18 |
copynumber.data.chr20 | CGHcall Example copynumber data hg18 chr20 |
copynumber.data.chr21 | CGHcall Example copynumber data hg18 chr21 |
CopyNumberBreakPointGenes | An S4 class to represent a CopyNumberBreakPointGenes object |
CopyNumberBreakPointGenes-class | An S4 class to represent a CopyNumberBreakPointGenes object |
CopyNumberBreakPoints | An S4 class to represent a CopyNumberBreakPoints object. |
CopyNumberBreakPoints-class | An S4 class to represent a CopyNumberBreakPoints object. |
ens.gene.ann.hg18 | Gene Annotation hg18 |
ens.gene.ann.hg19 | Gene Annotation hg19 |
ens.gene.ann.hg38 | Gene Annotation hg38 |
featureChromosomes | Access Object featureChromosomes. This method returns a vector with feature chromosomes. |
featureChromosomes-method | Access Object featureChromosomes. This method returns a vector with feature chromosomes. |
featureInfo | Access Options featureInfo. This method returns a dataframe with feature annotations. |
featureInfo-method | Access Options featureInfo. This method returns a dataframe with feature annotations. |
featuresPerGene | Access Object featuresPerGene. This method returns a vector with gene-related features for a particular gene. |
featuresPerGene-method | Access Object featuresPerGene. This method returns a vector with gene-related features for a particular gene. |
GeneBreak | GeneBreak: A package for gene breakpoint detection on copy number abberation data |
geneChromosomes | Access Object geneChromosomes. This method returns a vector with gene chromosomes. |
geneChromosomes-method | Access Object geneChromosomes. This method returns a vector with gene chromosomes. |
geneInfo | Access Options geneInfo. This method returns a dataframe with gene annotations. |
geneInfo-method | Access Options geneInfo. This method returns a dataframe with gene annotations. |
getBreakpoints | getBreakpoints |
namesFeatures | Access Object namesFeatures. This method returns a vector with feature names. |
namesFeatures-method | Access Object namesFeatures. This method returns a vector with feature names. |
recurrentGenes | Access Options recurrentGenes. This method returns a dataframe that contains genes that are recurrently affected across samples based on a FDR threshold. |
recurrentGenes-method | Access Options recurrentGenes. This method returns a dataframe that contains genes that are recurrently affected across samples based on a FDR threshold. |
sampleNames | Access Object sampleNames. This method returns a vector with sample names. |
sampleNames-method | Access Object sampleNames. This method returns a vector with sample names. |
segmentData | Access Object segmentData. This method returns a dataframe with segment values. |
segmentData-method | Access Object segmentData. This method returns a dataframe with segment values. |