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An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

Home Page: https://github.com/mcveanlab/DEploid

License: GNU General Public License v3.0

R 8.16% C++ 88.95% Shell 0.35% HTML 1.16% C 1.38%
mcmc deconvoluting-mixed-genomes cran unknown-proportions hmm malaria parasites phasing

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liuyingh alenzhao mcveanlab

deploid-r's Issues

wrinkles

Found the following hidden files and directories:
src/DEploid/lasso/.git
src/DEploid/lasso/.travis.yml
src/DEploid/lasso/.ci
src/DEploid/lasso/.circleci
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.

CRAN-pack does not know about
src/DEploid/lasso/.git
src/DEploid/lasso/.travis.yml
src/DEploid/lasso/.ci
src/DEploid/lasso/.circleci

adding filtering index into functions

Similar to

plotAltVsRef <- function(ref, alt, title = "Alt vs Ref",
                    exclude.ref = c(), exclude.alt = c(),
                    potentialOutliers = c(), cex.lab = 1, cex.main = 1,
                    cex.axis = 1){

Modify plotAltVsRefPlotly as

plotAltVsRefPlotly <- function(ref, alt, title = "Alt vs Ref",  potentialOutliers = c()){

Similarly, modify plotWSAFVsPLAFPlotly as

plotWSAFVsPLAFPlotly <- function(plaf, obsWSAF, ref, alt,
                                 title = "WSAF vs PLAF", potentialOutliers = c()){

compare to

plotWSAFvsPLAF <- function(plaf, obsWSAF, expWSAF = c(),
                      potentialOutliers = c(), title = "WSAF vs PLAF",
                      cex.lab = 1, cex.main = 1, cex.axis = 1){

update CRAN information on readme

It is recommended to use the current CRAN version. It can be installed from within R using

> install.packages('DEploid')

For the developing version, please install Rcpp package first. From the R-console, type

> install.packages("Rcpp")

Note:

If you are using Windows, please install Rtools from https://cran.r-project.org/bin/windows/Rtools/, then

> install.packages("devtools")
> library(devtools)
> install_github("mcveanlab/DEploid-r")

installation fails on windows machine ... 

> install.packages("C:/Users/Joe/Downloads/DEploid_0.3.1.tar.gz",respo=NULL)
Installing package into ‘C:/Users/Joe/Documents/R/win-library/3.3’
(as ‘lib’ is unspecified)
inferring 'repos = NULL' from 'pkgs'
* installing *source* package 'DEploid' ...
** libs

*** arch - i386
Warning: running command 'make -f "Makevars.win" -f "C:/PROGRA~1/R/R-33~1.1/etc/i386/Makeconf" -f "C:/PROGRA~1/R/R-33~1.1/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="DEploid.dll" ' had status 127
ERROR: compilation failed for package 'DEploid'
* removing 'C:/Users/Joe/Documents/R/win-library/3.3/DEploid'
Warning messages:
1: running command '"C:/PROGRA~1/R/R-33~1.1/bin/x64/R" CMD INSTALL -l "C:\Users\Joe\Documents\R\win-library\3.3" "C:/Users/Joe/Downloads/DEploid_0.3.1.tar.gz"' had status 1 
2: In install.packages("C:/Users/Joe/Downloads/DEploid_0.3.1.tar.gz",  :
  installation of package ‘C:/Users/Joe/Downloads/DEploid_0.3.1.tar.gz’ had non-zero exit status
>

cran windows error

  • installing source package 'DEploid' ...
    ** using staged installation
    ** libs

*** arch - i386
d:/Compiler/rtools40/mingw32/bin/g++ -std=gnu++11 -I"D:/RCompile/recent/R4/include" -DNDEBUG -I'd:/RCompile/CRANpkg/lib/4.0gcc8/Rcpp/include' -I"d:/Compiler/gcc-4.9.3/local330/include" -I/usr/share/R/include/ -IDEploid/ -IDEploid/codeCogs/ -IDEploid/random/ -IDEploid/gzstream/ -IDEploid/lasso/ -DVERSION=""R"" -DRBUILD -O2 -Wall -mtune=core2 -c rvcf.cpp -o rvcf.o
In file included from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/combaseapi.h:155,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/objbase.h:14,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/ole2.h:17,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/wtypes.h:12,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/winscard.h:10,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/windows.h:97,
from d:/Compiler/gcc-4.9.3/local330/include/zconf.h:329,
from d:/Compiler/gcc-4.9.3/local330/include/zlib.h:34,
from DEploid/gzstream/gzstream.h:36,
from DEploid/vcfReader.hpp:32,
from rvcf.cpp:2:
D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/objidlbase.h:864:18: error: macro "Realloc" requires 3 arguments, but only 2 given
SIZE_T cb) = 0;
^
In file included from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/combaseapi.h:155,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/objbase.h:14,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/ole2.h:17,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/wtypes.h:12,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/winscard.h:10,
from D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/windows.h:97,
from d:/Compiler/gcc-4.9.3/local330/include/zconf.h:329,
from d:/Compiler/gcc-4.9.3/local330/include/zlib.h:34,
from DEploid/gzstream/gzstream.h:36,
from DEploid/vcfReader.hpp:32,
from rvcf.cpp:2:
D:/Compiler/rtools40/mingw32/i686-w64-mingw32/include/objidlbase.h:864:22: error: 'Realloc' declared as a 'virtual' field
SIZE_T cb) = 0;
^
In file included from D:/RCompile/recent/R4/include/R.h:91,
from d:/RCompile/CRANpkg/lib/4.0gcc8/Rcpp/include/Rcpp/r/headers.h:71,
from d:/RCompile/CRANpkg/lib/4.0gcc8/Rcpp/include/RcppCommon.h:29,
from d:/RCompile/CRANpkg/lib/4.0gcc8/Rcpp/include/Rcpp.h:27,
from rvcf.cpp:1:
D:/RCompile/recent/R4/include/R_ext/RS.h:74:37: error: expected identifier before '(' token
#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
^
D:/RCompile/recent/R4/include/R_ext/RS.h:74:37: error: 'parameter' declared as function returning a function
D:/RCompile/recent/R4/include/R_ext/RS.h:74:50: error: expected ')' before ',' token
#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
~ ^
D:/RCompile/recent/R4/include/R_ext/RS.h:74:37: error: expected identifier before '(' token
#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
^
D:/RCompile/recent/R4/include/R_ext/RS.h:74:37: error: 'parameter' declared as function returning a function
D:/RCompile/recent/R4/include/R_ext/RS.h:74:50: error: expected ')' before ',' token
#define Free(p) (R_chk_free( (void *)(p) ), (p) = NULL)
~ ^
make: *** [D:/RCompile/recent/R4/etc/i386/Makeconf:215: rvcf.o] Error 1
ERROR: compilation failed for package 'DEploid'

  • removing 'd:/RCompile/CRANincoming/R-devel/lib/DEploid'

import htmlwidgets

Dear maintainers,

This concerns the CRAN packages

AFM ASGS.foyer BayesianTools Cyclops DEploid DescribeDisplay
EBMAforecast EValue EcoGenetics FSA FedData FuzzyAHP GBJ GGally Gmisc
KFAS MetaComp NetLogoR PRROC ParamHelpers PeakSegOptimal PivotalR
REddyProc RItools RNifti RStoolbox RcmdrPlugin.lfstat SensMap SpaDES
SpaDES.core SpaDES.tools SuperLearner TOSTER aprof batchtools
bayesboot biomartr bnclassify bomrang brms

maintained by one of you:

$DEploid
'::' or ':::' import not declared from: ‘htmlwidgets’

Clear association between proportions and haplotypes

Hi!
I've testing out dEploid for some "off label" uses-- namely, for mitochondrial mixture deconvolution in forensics, and so far the results of your program are promising. I'm currently testing out the R interface as we already have a code-base in R and I was wondering if some aspects of the documentation could be more clear. For example, the R object returned from dEploid has some fields that could have a little more information on them. In particular, the $Haps matrix appears to have 1 row for each inferred haplotype-- I take it that 1 means the alternative allele, 0 means the reference? And the proportions matrix appears to give the mixture proportions for each round of the MCMC. How, then, are the mixture proportions re-associated back to the haplotype? In our test-case there's only three inferred haplotypes and five columns of proportions so the correspondence does not seem clear.
Regardless, I love the program so far!
-August

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