patternCNV-package: patternCNV: a versatile tool for detecting copy number...

Description Details Author(s) References Examples

Description

PatternCNV is a versatile tool to facilitate CNV detection and interpretation from either Germline or Tumor/Normal pairs of Exome-seq samples. The idea behind proposed patternCNV approach is to summarize common coverage trends of a same exome capture-kit, and then facilitate accurate CNV estimation. Across multiple control-samples (i.e. germline), we proposed to summarize average and variability of exon-coverage, defined as "average-pattern" and "variability-pattern", respectively. Then, exon-level CNV is reliably estimated by computing difference between observed read-depth and expected coverage

Details

Package: patternCNV
Type: Package
Version: 0.99.2
Date: 2013-12-18
License: Artistic-2.0
Depends: methods, GenomicRanges, IRanges

Author(s)

Chen Wang

Maintainer: Chen Wang <[email protected]> or <[email protected]>

References

PatternCNV: a versatile tool for detecting copy number changes from exome sequencing data (submitted)

Examples

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#=== load a simulation example
config.filename <- 'sim1.ini'
makeSimulation(config.filename)
sim.session <- createSession(config.filename)

#=== print summary information of created patternCNV session
summary(sim.session)

hshdndx/new-to-CNV documentation built on May 16, 2017, 11:26 p.m.