LDExplorer: Efficient Whole-Genome LD Based Haplotpe Block Recognition

Share:

LDExplorer is an R package for the memory and time efficient whole-genome LD based haplotype block recognition.

Author
Daniel Taliun <Daniel.Taliun@eurac.edu>, Johann Gamper<gamper@inf.unibz.it>, Cristian Pattaro <Cristian.Pattaro@eurac.edu>
Date of publication
2013-11-25 10:11:40
Maintainer
Daniel Taliun <Daniel.Taliun@eurac.edu>
License
GPL (>=3)
Version
1.0.3

View on R-Forge

Man pages

create_browser_track
BED file generation for UCSC and Ensembl genome browsers.
ld
Linkage disequilibrium (LD) computation from phased data
mig
Memory-efficient Implementation of Gabriel et al. 2002...
mig_multi_chr
Memory-efficient Implementation of Gabriel et al. 2002...
mig_multi_regions
Memory-efficient Implementation of Gabriel et al. 2002...
mig_rsq
Memory-efficient Implementation of Gabriel et al. 2002...

Files in this package

LDExplorer/COPYING
LDExplorer/DESCRIPTION
LDExplorer/NAMESPACE
LDExplorer/R
LDExplorer/R/CREATE_BROWSER_TRACK.R
LDExplorer/R/LD.R
LDExplorer/R/MIG.R
LDExplorer/R/MIG_MULTI_CHR.R
LDExplorer/R/MIG_MULTI_REGIONS.R
LDExplorer/R/MIG_RSQ.R
LDExplorer/inst
LDExplorer/inst/doc
LDExplorer/inst/doc/1000G_phase1_v3_20101123_CEU_chr2_89153688_89307566.vcf.gz
LDExplorer/inst/doc/HapMapII_r22_CEU_chr20_31767872_33700401.legend.txt.gz
LDExplorer/inst/doc/HapMapII_r22_CEU_chr20_31767872_33700401.phase.gz
LDExplorer/man
LDExplorer/man/create_browser_track.Rd
LDExplorer/man/ld.Rd
LDExplorer/man/mig.Rd
LDExplorer/man/mig_multi_chr.Rd
LDExplorer/man/mig_multi_regions.Rd
LDExplorer/man/mig_rsq.Rd
LDExplorer/src
LDExplorer/src/LDExplorer.cpp
LDExplorer/src/LDExplorer.h
LDExplorer/src/Makevars
LDExplorer/src/Makevars.win
LDExplorer/src/algorithms
LDExplorer/src/algorithms/Algorithm.cpp
LDExplorer/src/algorithms/AlgorithmFactory.cpp
LDExplorer/src/algorithms/AlgorithmMIG.cpp
LDExplorer/src/algorithms/AlgorithmMIGP.cpp
LDExplorer/src/algorithms/AlgorithmMIGPP.cpp
LDExplorer/src/algorithms/CI.cpp
LDExplorer/src/algorithms/CIAV.cpp
LDExplorer/src/algorithms/CIFactory.cpp
LDExplorer/src/algorithms/CIWP.cpp
LDExplorer/src/algorithms/LD.cpp
LDExplorer/src/algorithms/Makefile
LDExplorer/src/algorithms/Partition.cpp
LDExplorer/src/algorithms/include
LDExplorer/src/algorithms/include/Algorithm.h
LDExplorer/src/algorithms/include/AlgorithmFactory.h
LDExplorer/src/algorithms/include/AlgorithmMIG.h
LDExplorer/src/algorithms/include/AlgorithmMIGP.h
LDExplorer/src/algorithms/include/AlgorithmMIGPP.h
LDExplorer/src/algorithms/include/CI.h
LDExplorer/src/algorithms/include/CIAV.h
LDExplorer/src/algorithms/include/CIFactory.h
LDExplorer/src/algorithms/include/CIWP.h
LDExplorer/src/algorithms/include/LD.h
LDExplorer/src/algorithms/include/Partition.h
LDExplorer/src/auxiliary
LDExplorer/src/auxiliary/Makefile
LDExplorer/src/auxiliary/auxiliary.cpp
LDExplorer/src/auxiliary/include
LDExplorer/src/auxiliary/include/auxiliary.h
LDExplorer/src/db
LDExplorer/src/db/Db.cpp
LDExplorer/src/db/DbView.cpp
LDExplorer/src/db/Makefile
LDExplorer/src/db/Unique.cpp
LDExplorer/src/db/include
LDExplorer/src/db/include/Db.h
LDExplorer/src/db/include/DbView.h
LDExplorer/src/db/include/Unique.h
LDExplorer/src/exception
LDExplorer/src/exception/Exception.cpp
LDExplorer/src/exception/Makefile
LDExplorer/src/exception/include
LDExplorer/src/exception/include/Exception.h
LDExplorer/src/reader
LDExplorer/src/reader/GzipReader.cpp
LDExplorer/src/reader/Makefile
LDExplorer/src/reader/Reader.cpp
LDExplorer/src/reader/ReaderFactory.cpp
LDExplorer/src/reader/TextReader.cpp
LDExplorer/src/reader/include
LDExplorer/src/reader/include/GzipReader.h
LDExplorer/src/reader/include/Reader.h
LDExplorer/src/reader/include/ReaderFactory.h
LDExplorer/src/reader/include/TextReader.h
LDExplorer/src/writer
LDExplorer/src/writer/GzipWriter.cpp
LDExplorer/src/writer/Makefile
LDExplorer/src/writer/TextWriter.cpp
LDExplorer/src/writer/Writer.cpp
LDExplorer/src/writer/WriterFactory.cpp
LDExplorer/src/writer/include
LDExplorer/src/writer/include/GzipWriter.h
LDExplorer/src/writer/include/TextWriter.h
LDExplorer/src/writer/include/Writer.h
LDExplorer/src/writer/include/WriterFactory.h
LDExplorer/src/zlib
LDExplorer/src/zlib/Makefile
LDExplorer/src/zlib/adler32.c
LDExplorer/src/zlib/compress.c
LDExplorer/src/zlib/crc32.c
LDExplorer/src/zlib/crc32.h
LDExplorer/src/zlib/deflate.c
LDExplorer/src/zlib/deflate.h
LDExplorer/src/zlib/gzclose.c
LDExplorer/src/zlib/gzguts.h
LDExplorer/src/zlib/gzlib.c
LDExplorer/src/zlib/gzread.c
LDExplorer/src/zlib/gzwrite.c
LDExplorer/src/zlib/infback.c
LDExplorer/src/zlib/inffast.c
LDExplorer/src/zlib/inffast.h
LDExplorer/src/zlib/inffixed.h
LDExplorer/src/zlib/inflate.c
LDExplorer/src/zlib/inflate.h
LDExplorer/src/zlib/inftrees.c
LDExplorer/src/zlib/inftrees.h
LDExplorer/src/zlib/trees.c
LDExplorer/src/zlib/trees.h
LDExplorer/src/zlib/uncompr.c
LDExplorer/src/zlib/zconf.h
LDExplorer/src/zlib/zlib.h
LDExplorer/src/zlib/zutil.c
LDExplorer/src/zlib/zutil.h