DEploid: Deconvolute Mixed Genomes with Unknown Proportions
Version 0.3.2

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.

AuthorJoe Zhu [aut, cre, cph]
Date of publication2016-11-25 19:47:49
MaintainerJoe Zhu <joe.zhu@well.ox.ac.uk>
LicenseGPL (>= 3)
Version0.3.2
URL https://github.com/mcveanlab/DEploid-r
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DEploid")

Getting started

README.md
Command Line Arguments

Popular man pages

computeObsWSAF: Compute observed WSAF
extractCoverageFromTxt: Extract read counts from plain text file
extractPLAF: Extract PLAF
haplotypePainter: Painting haplotype according the reference panel
histWSAF: WSAF histogram
plotObsExpWSAF: Plot WSAF
plotProportions: Plot proportions
See all...

All man pages Function index File listing

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

Functions

computeObsWSAF Man page Source code
dEploid Man page Source code
extractCoverageFromTxt Man page Source code
extractCoverageFromVcf Man page Source code
extractPLAF Man page Source code
haplotypePainter Man page Source code
histWSAF Man page Source code
plotAltVsRef Man page Source code
plotObsExpWSAF Man page Source code
plotProportions Man page Source code
plotWSAFvsPLAF Man page Source code
test_RRG_sample Source code
test_RRG_sampleExpoExpoLimit Source code
test_RRG_sampleUnitExpo Source code

Files

inst
inst/extdata
inst/extdata/labStrains.test.PLAF.txt
inst/extdata/labStrains.test.exclude.txt
inst/extdata/PG0390-C.test.vcf.gz
inst/extdata/labStrains.test.panel.txt
inst/extdata/PG0390-C.test.alt
inst/extdata/PG0390-C.test.ref
inst/doc
inst/doc/dEploid-Arguments.Rmd
inst/doc/dEploid-Arguments.R
inst/doc/dEploid-Arguments.html
tests
tests/testthat.R
tests/testthat
tests/testthat/test-r_random-generator.R
tests/testthat/test-DEploid_tools.R
tests/testthat/test-dEploid.R
src
src/Makevars
src/r_random_generator.h
src/DEploid
src/DEploid/utility.cpp
src/DEploid/updateHap.cpp
src/DEploid/debug
src/DEploid/debug/mcmcDebug.cpp
src/DEploid/debug/vcfReaderDebug.cpp
src/DEploid/random
src/DEploid/random/mersenne_twister.hpp
src/DEploid/random/mersenne_twister.cpp
src/DEploid/random/fastfunc.cpp
src/DEploid/random/fastfunc.hpp
src/DEploid/random/random_generator.hpp
src/DEploid/random/random_generator.cpp
src/DEploid/dEploid.cpp
src/DEploid/mcmc.cpp
src/DEploid/variantIndex.hpp
src/DEploid/variantIndex.cpp
src/DEploid/updateHap.hpp
src/DEploid/dEploidIO.cpp
src/DEploid/mcmc.hpp
src/DEploid/export
src/DEploid/export/dEploidIOExport.cpp
src/DEploid/export/dEploidIOExportPosteriorProb.cpp
src/DEploid/dEploidIO.hpp
src/DEploid/global.h
src/DEploid/panel.hpp
src/DEploid/vcfReader.cpp
src/DEploid/gzstream
src/DEploid/gzstream/index.html
src/DEploid/gzstream/COPYING.LIB
src/DEploid/gzstream/test_gzip.C
src/DEploid/gzstream/version
src/DEploid/gzstream/README
src/DEploid/gzstream/logo.gif
src/DEploid/gzstream/test_gunzip.C
src/DEploid/gzstream/gzstream.cpp
src/DEploid/gzstream/gzstream.h
src/DEploid/utility.hpp
src/DEploid/txtReader.cpp
src/DEploid/exceptions.hpp
src/DEploid/txtReader.hpp
src/DEploid/codeCogs
src/DEploid/codeCogs/errorfnc.h
src/DEploid/codeCogs/mersenne.hpp
src/DEploid/codeCogs/expx2.h
src/DEploid/codeCogs/xsub_ln_add1.h
src/DEploid/codeCogs/log_gamma.h
src/DEploid/codeCogs/poly_eval.h
src/DEploid/codeCogs/errorfn.h
src/DEploid/codeCogs/machine_epsilon.h
src/DEploid/codeCogs/errorfnc_exp.h
src/DEploid/codeCogs/loggammasum.h
src/DEploid/codeCogs/loggammafrac.h
src/DEploid/codeCogs/stirling.h
src/DEploid/codeCogs/randomSample.hpp
src/DEploid/codeCogs/logbeta.h
src/DEploid/codeCogs/gamma.h
src/DEploid/codeCogs/ln_add1.h
src/DEploid/codeCogs/asympt_expn.h
src/DEploid/panel.cpp
src/DEploid/vcfReader.hpp
src/test_exports.cpp
src/Makevars.win
src/RcppExports.cpp
src/dEploidr.cpp
NAMESPACE
R
R/DEploidR.R
R/dEploid.R
R/RcppExports.R
vignettes
vignettes/dEploid-Arguments.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/plotWSAFvsPLAF.Rd
man/plotAltVsRef.Rd
man/plotObsExpWSAF.Rd
man/histWSAF.Rd
man/plotProportions.Rd
man/haplotypePainter.Rd
man/extractPLAF.Rd
man/computeObsWSAF.Rd
man/dEploid.Rd
man/extractCoverageFromTxt.Rd
man/extractCoverageFromVcf.Rd
DEploid documentation built on May 19, 2017, 7:52 a.m.

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