Man pages for hshdndx/new-to-CNV
patternCNV: a versatile tool for detecting copy number changes from exome-seq data

avgExonCoverageCompute average coverage of exons across samples
chrCoverageQCQuality-check exome coverage across chromosomes
cnvMatrixRetrieve CNV matrix
computeMultiCNVCompute copy number variation (CNV) for multiple samples
computeSingleCNVCompute copy number variation (CNV) for single sample
coverageMatrixRetrieve coverage matrix
createSessionCreate patternCNV session object
estimateFDREstimate false discovery rate of copy number variation...
exonInfoRetrieve exon information
exonNumNumber of exons
exportCNVtableExports exon-level CNV information as per-sample tables
fdrMatrixRetrieve FDR matrix
fitNullModelFit Null distribution of copy number variation signals
geneCoverageQCQuality-check exon-coverage of given genes
hg19.Chr_length_vecLength of chr1-22 according to hg19
learnPatternsLearn average and variability patterns
makeSimulationMake patternCNV simulation files for easy testing
PatCNVData-classClass '"PatCNVData"'
PatCNVSession-classClass '"PatCNVSession"'
patternCNV-packagepatternCNV: a versatile tool for detecting copy number...
plotAutosomeCNVGenerate autosome (chr1-22) CNV plot of given sample
plotChrCNVGenerate chromosome-level CNV plot of given sample
plotGeneHeatmapGenerate CNV heatmap of given genes
sampleCoverageSummarize sample coverage
sampleInfoRetrieve sample information
sampleNumNumber of samples
scanMultiCovgScan exome coverage of multiple samples
scanSingleCovgScan exome coverage of single sample
segmentCNVOutput CNV segmentation results
show-methodsGeneric Methods for Function 'show'
sim.cnvDatasimulated data of "PatCNVData" class with coverage and CNV...
sim.covgDatasimulated data of "PatCNVData" class with coverage...
summary-methodsGeneric Methods for Function 'summary'
hshdndx/new-to-CNV documentation built on May 17, 2019, 5:55 p.m.