DEploid: Deconvolute Mixed Genomes with Unknown Proportions

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Traditional phasing programs are limited to diploid organisms. Our method modifies Li and Stephens algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haplotype searches in a multiple infection setting. This package is primarily developed as part of the Pf3k project, which is a global collaboration using the latest sequencing technologies to provide a high-resolution view of natural variation in the malaria parasite Plasmodium falciparum. Parasite DNA are extracted from patient blood sample, which often contains more than one parasite strain, with unknown proportions. This package is used for deconvoluting mixed haplotypes, and reporting the mixture proportions from each sample.

Author
Joe Zhu [aut, cre, cph]
Date of publication
2016-11-25 19:47:49
Maintainer
Joe Zhu <joe.zhu@well.ox.ac.uk>
License
GPL (>= 3)
Version
0.3.2
URLs

View on CRAN

Man pages

computeObsWSAF
Compute observed WSAF
dEploid
Deconvolute mixed haplotypes
extractCoverageFromTxt
Extract read counts from plain text file
extractCoverageFromVcf
Extract read counts from VCF
extractPLAF
Extract PLAF
haplotypePainter
Painting haplotype according the reference panel
histWSAF
WSAF histogram
plotAltVsRef
Plot coverage
plotObsExpWSAF
Plot WSAF
plotProportions
Plot proportions
plotWSAFvsPLAF
Plot WSAF vs PLAF

Files in this package

DEploid
DEploid/inst
DEploid/inst/extdata
DEploid/inst/extdata/labStrains.test.PLAF.txt
DEploid/inst/extdata/labStrains.test.exclude.txt
DEploid/inst/extdata/PG0390-C.test.vcf.gz
DEploid/inst/extdata/labStrains.test.panel.txt
DEploid/inst/extdata/PG0390-C.test.alt
DEploid/inst/extdata/PG0390-C.test.ref
DEploid/inst/doc
DEploid/inst/doc/dEploid-Arguments.Rmd
DEploid/inst/doc/dEploid-Arguments.R
DEploid/inst/doc/dEploid-Arguments.html
DEploid/tests
DEploid/tests/testthat.R
DEploid/tests/testthat
DEploid/tests/testthat/test-r_random-generator.R
DEploid/tests/testthat/test-DEploid_tools.R
DEploid/tests/testthat/test-dEploid.R
DEploid/src
DEploid/src/Makevars
DEploid/src/r_random_generator.h
DEploid/src/DEploid
DEploid/src/DEploid/utility.cpp
DEploid/src/DEploid/updateHap.cpp
DEploid/src/DEploid/debug
DEploid/src/DEploid/debug/mcmcDebug.cpp
DEploid/src/DEploid/debug/vcfReaderDebug.cpp
DEploid/src/DEploid/random
DEploid/src/DEploid/random/mersenne_twister.hpp
DEploid/src/DEploid/random/mersenne_twister.cpp
DEploid/src/DEploid/random/fastfunc.cpp
DEploid/src/DEploid/random/fastfunc.hpp
DEploid/src/DEploid/random/random_generator.hpp
DEploid/src/DEploid/random/random_generator.cpp
DEploid/src/DEploid/dEploid.cpp
DEploid/src/DEploid/mcmc.cpp
DEploid/src/DEploid/variantIndex.hpp
DEploid/src/DEploid/variantIndex.cpp
DEploid/src/DEploid/updateHap.hpp
DEploid/src/DEploid/dEploidIO.cpp
DEploid/src/DEploid/mcmc.hpp
DEploid/src/DEploid/export
DEploid/src/DEploid/export/dEploidIOExport.cpp
DEploid/src/DEploid/export/dEploidIOExportPosteriorProb.cpp
DEploid/src/DEploid/dEploidIO.hpp
DEploid/src/DEploid/global.h
DEploid/src/DEploid/panel.hpp
DEploid/src/DEploid/vcfReader.cpp
DEploid/src/DEploid/gzstream
DEploid/src/DEploid/gzstream/index.html
DEploid/src/DEploid/gzstream/COPYING.LIB
DEploid/src/DEploid/gzstream/test_gzip.C
DEploid/src/DEploid/gzstream/version
DEploid/src/DEploid/gzstream/README
DEploid/src/DEploid/gzstream/logo.gif
DEploid/src/DEploid/gzstream/test_gunzip.C
DEploid/src/DEploid/gzstream/gzstream.cpp
DEploid/src/DEploid/gzstream/gzstream.h
DEploid/src/DEploid/utility.hpp
DEploid/src/DEploid/txtReader.cpp
DEploid/src/DEploid/exceptions.hpp
DEploid/src/DEploid/txtReader.hpp
DEploid/src/DEploid/codeCogs
DEploid/src/DEploid/codeCogs/errorfnc.h
DEploid/src/DEploid/codeCogs/mersenne.hpp
DEploid/src/DEploid/codeCogs/expx2.h
DEploid/src/DEploid/codeCogs/xsub_ln_add1.h
DEploid/src/DEploid/codeCogs/log_gamma.h
DEploid/src/DEploid/codeCogs/poly_eval.h
DEploid/src/DEploid/codeCogs/errorfn.h
DEploid/src/DEploid/codeCogs/machine_epsilon.h
DEploid/src/DEploid/codeCogs/errorfnc_exp.h
DEploid/src/DEploid/codeCogs/loggammasum.h
DEploid/src/DEploid/codeCogs/loggammafrac.h
DEploid/src/DEploid/codeCogs/stirling.h
DEploid/src/DEploid/codeCogs/randomSample.hpp
DEploid/src/DEploid/codeCogs/logbeta.h
DEploid/src/DEploid/codeCogs/gamma.h
DEploid/src/DEploid/codeCogs/ln_add1.h
DEploid/src/DEploid/codeCogs/asympt_expn.h
DEploid/src/DEploid/panel.cpp
DEploid/src/DEploid/vcfReader.hpp
DEploid/src/test_exports.cpp
DEploid/src/Makevars.win
DEploid/src/RcppExports.cpp
DEploid/src/dEploidr.cpp
DEploid/NAMESPACE
DEploid/R
DEploid/R/DEploidR.R
DEploid/R/dEploid.R
DEploid/R/RcppExports.R
DEploid/vignettes
DEploid/vignettes/dEploid-Arguments.Rmd
DEploid/README.md
DEploid/MD5
DEploid/build
DEploid/build/vignette.rds
DEploid/DESCRIPTION
DEploid/man
DEploid/man/plotWSAFvsPLAF.Rd
DEploid/man/plotAltVsRef.Rd
DEploid/man/plotObsExpWSAF.Rd
DEploid/man/histWSAF.Rd
DEploid/man/plotProportions.Rd
DEploid/man/haplotypePainter.Rd
DEploid/man/extractPLAF.Rd
DEploid/man/computeObsWSAF.Rd
DEploid/man/dEploid.Rd
DEploid/man/extractCoverageFromTxt.Rd
DEploid/man/extractCoverageFromVcf.Rd