genoCN: genotyping and copy number study tools

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Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations

Author
Wei Sun and ZhengZheng Tang
Date of publication
None
Maintainer
Wei Sun <wsun@bios.unc.edu>
License
GPL (>=2)
Version
1.26.0

View on Bioconductor

Man pages

code.genotype
code bi-allele genotype to numerical value
genoCNA
Copy Number Aberration
genoCNV
Copy Number Variation
init.Para.CNA
Initial parameters for the HMM
init.Para.CNV
Initial parameters for the HMM of genoCNV
plotCN
plot LRR, BAF, and the copy number estimates
snpData
Simulated LRR and BAF data for 17,348 SNPs on chromosome 22.
snpInfo
Information of 17,348 SNPs on chromosome 22.

Files in this package

genoCN/DESCRIPTION
genoCN/NAMESPACE
genoCN/R
genoCN/R/backward.R
genoCN/R/baum.welch.R
genoCN/R/check.para.R
genoCN/R/code.genotype.R
genoCN/R/estimate.para.R
genoCN/R/extract.postP.R
genoCN/R/genoCNA.R
genoCN/R/genoCNV.R
genoCN/R/get.weights.R
genoCN/R/output.R
genoCN/R/plotCN.R
genoCN/R/print.para.genoCN.R
genoCN/R/utility.R
genoCN/R/viterbi.R
genoCN/build
genoCN/build/vignette.rds
genoCN/data
genoCN/data/init.Para.CNA.rda
genoCN/data/init.Para.CNV.rda
genoCN/data/snpData.rda
genoCN/data/snpInfo.rda
genoCN/inst
genoCN/inst/NEWS
genoCN/inst/doc
genoCN/inst/doc/genoCN.R
genoCN/inst/doc/genoCN.Rnw
genoCN/inst/doc/genoCN.pdf
genoCN/man
genoCN/man/code.genotype.Rd
genoCN/man/genoCNA.Rd
genoCN/man/genoCNV.Rd
genoCN/man/init.Para.CNA.Rd
genoCN/man/init.Para.CNV.Rd
genoCN/man/plotCN.Rd
genoCN/man/snpData.Rd
genoCN/man/snpInfo.Rd
genoCN/src
genoCN/src/tnorm_mle.c
genoCN/src/tnorm_mle.h
genoCN/src/utility.c
genoCN/src/utility.h
genoCN/src/xCNV.c
genoCN/src/xCNV.h
genoCN/test
genoCN/test/get.init.Para.CNA.R
genoCN/test/get.init.Para.CNV.R
genoCN/test/simulate.R
genoCN/test/test_real_data.R
genoCN/test/test_simu_data.R
genoCN/test/tnorm.mle.R
genoCN/vignettes
genoCN/vignettes/genoCN.Rnw
genoCN/vignettes/simu_data.png
genoCN/vignettes/simu_data_genoCN.png