Man pages for hshdndx/new-to-CNV
patternCNV: a versatile tool for detecting copy number changes from exome-seq data
| avgExonCoverage | Compute average coverage of exons across samples |
| chrCoverageQC | Quality-check exome coverage across chromosomes |
| cnvMatrix | Retrieve CNV matrix |
| computeMultiCNV | Compute copy number variation (CNV) for multiple samples |
| computeSingleCNV | Compute copy number variation (CNV) for single sample |
| coverageMatrix | Retrieve coverage matrix |
| createSession | Create patternCNV session object |
| estimateFDR | Estimate false discovery rate of copy number variation... |
| exonInfo | Retrieve exon information |
| exonNum | Number of exons |
| exportCNVtable | Exports exon-level CNV information as per-sample tables |
| fdrMatrix | Retrieve FDR matrix |
| fitNullModel | Fit Null distribution of copy number variation signals |
| geneCoverageQC | Quality-check exon-coverage of given genes |
| hg19.Chr_length_vec | Length of chr1-22 according to hg19 |
| learnPatterns | Learn average and variability patterns |
| makeSimulation | Make patternCNV simulation files for easy testing |
| PatCNVData-class | Class '"PatCNVData"' |
| PatCNVSession-class | Class '"PatCNVSession"' |
| patternCNV-package | patternCNV: a versatile tool for detecting copy number... |
| plotAutosomeCNV | Generate autosome (chr1-22) CNV plot of given sample |
| plotChrCNV | Generate chromosome-level CNV plot of given sample |
| plotGeneHeatmap | Generate CNV heatmap of given genes |
| sampleCoverage | Summarize sample coverage |
| sampleInfo | Retrieve sample information |
| sampleNum | Number of samples |
| scanMultiCovg | Scan exome coverage of multiple samples |
| scanSingleCovg | Scan exome coverage of single sample |
| segmentCNV | Output CNV segmentation results |
| show-methods | Generic Methods for Function 'show' |
| sim.cnvData | simulated data of "PatCNVData" class with coverage and CNV... |
| sim.covgData | simulated data of "PatCNVData" class with coverage... |
| summary-methods | Generic Methods for Function 'summary' |
