Files in DEploid

Deconvolute Mixed Genomes with Unknown Proportions

MD5

README.md

NAMESPACE

DESCRIPTION

build/vignette.rds

src/dEploidr.cpp

src/r_random_generator.h

src/Makevars.win

src/RcppExports.cpp

src/test_exports.cpp

src/init.c

src/Makevars

src/rvcf.cpp

src/DEploid/panel.cpp

src/DEploid/vcfReader.cpp

src/DEploid/ibd.hpp

src/DEploid/exceptions.hpp

src/DEploid/dEploidIO.hpp

src/DEploid/txtReader.hpp

src/DEploid/panel.hpp

src/DEploid/variantIndex.cpp

src/DEploid/chooseK.hpp

src/DEploid/dEploidIO.cpp

src/DEploid/txtReader.cpp

src/DEploid/chooseK.cpp

src/DEploid/global.hpp

src/DEploid/updateHap.hpp

src/DEploid/mcmc.hpp

src/DEploid/variantIndex.hpp

src/DEploid/utility.cpp

src/DEploid/vcfReader.hpp

src/DEploid/ibd.cpp

src/DEploid/mcmc.cpp

src/DEploid/updateHap.cpp

src/DEploid/utility.hpp

src/DEploid/debug/vcfReaderDebug.cpp

src/DEploid/debug/mcmcDebug.cpp

src/DEploid/gzstream/index.html

src/DEploid/gzstream/test_gunzip.C

src/DEploid/gzstream/gzstream.h

src/DEploid/gzstream/logo.gif

src/DEploid/gzstream/test_gzip.C

src/DEploid/gzstream/gzstream.cpp

src/DEploid/gzstream/README

src/DEploid/gzstream/COPYING.LIB

src/DEploid/codeCogs/loggammafrac.h

src/DEploid/codeCogs/poly_eval.h

src/DEploid/codeCogs/errorfnc_exp.h

src/DEploid/codeCogs/xsub_ln_add1.h

src/DEploid/codeCogs/errorfn.h

src/DEploid/codeCogs/gamma.h

src/DEploid/codeCogs/machine_epsilon.h

src/DEploid/codeCogs/logbeta.h

src/DEploid/codeCogs/log_gamma.h

src/DEploid/codeCogs/ln_add1.h

src/DEploid/codeCogs/randomSample.hpp

src/DEploid/codeCogs/expx2.h

src/DEploid/codeCogs/asympt_expn.h

src/DEploid/codeCogs/loggammasum.h

src/DEploid/codeCogs/stirling.h

src/DEploid/codeCogs/errorfnc.h

src/DEploid/codeCogs/mersenne.hpp

src/DEploid/lasso/dEploidLasso.cpp

src/DEploid/lasso/dEploidLasso.hpp

src/DEploid/lasso/lasso.hpp

src/DEploid/lasso/dbgmacro.hpp

src/DEploid/lasso/lasso.cpp

src/DEploid/lasso/lassoDBG.cpp

src/DEploid/lasso/src/dEploidLasso.cpp

src/DEploid/lasso/src/lassoOut.cpp

src/DEploid/lasso/src/main.cpp

src/DEploid/lasso/src/dEploidLasso.hpp

src/DEploid/lasso/src/lasso.hpp

src/DEploid/lasso/src/dbgmacro.hpp

src/DEploid/lasso/src/lasso.cpp

src/DEploid/lasso/src/lassoDBG.cpp

src/DEploid/random/mersenne_twister.hpp

src/DEploid/random/fastfunc.hpp

src/DEploid/random/random_generator.cpp

src/DEploid/random/mersenne_twister.cpp

src/DEploid/random/fastfunc.cpp

src/DEploid/random/random_generator.hpp

src/DEploid/export/dEploidIOExportPosteriorProb.cpp

src/DEploid/export/dEploidIOExport.cpp

src/DEploid/export/writeMcmcRelated.cpp

R/dEploidPlotly.R R/dEploid.R R/RcppExports.R R/DEploidR.R vignettes/dEploid-Arguments.Rmd man/extractPLAF.Rd man/extractCoverageFromTxt.Rd man/plotObsExpWSAFPlotly.Rd man/computeObsWSAF.Rd man/plotWSAFVsPLAFPlotly.Rd man/plotProportions.Rd man/plotWSAFvsPLAF.Rd man/extractCoverageFromVcf.Rd man/DEploid-package.Rd man/plotHistWSAFPlotly.Rd man/extractVcf.Rd man/plotObsExpWSAF.Rd man/plotAltVsRef.Rd man/plotAltVsRefPlotly.Rd man/dEploid.Rd man/histWSAF.Rd man/haplotypePainter.Rd tests/testthat.R tests/testthat/test-r_random-generator.R tests/testthat/test-dEploid.R tests/testthat/test-DEploid_tools.R

inst/CITATION

inst/doc/dEploid-Arguments.R inst/doc/dEploid-Arguments.Rmd

inst/doc/dEploid-Arguments.html

inst/extdata/deploid.png

inst/extdata/labStrains.test.exclude.txt

inst/extdata/labStrains.test.panel.txt

inst/extdata/PG0390-C.test.vcf.gz

inst/extdata/PG0390-C.test.alt

inst/extdata/PG0390-C.test.ref

inst/extdata/labStrains.test.PLAF.txt

DEploid documentation built on April 22, 2020, 1:04 a.m.