GWAtoolbox: GWAS Quality Control

Controls for duplicated IDs, distribution of betas, SEs, etc.

AuthorDaniel Taliun <Daniel.Taliun@eurac.edu>, Christian Fuchsberger <cfuchsb@umich.edu>, Cristian Pattaro <Cristian.Pattaro@eurac.edu>
Date of publication2015-05-18 20:03:20
MaintainerDaniel Taliun <Daniel.Taliun@eurac.edu>
LicenseGPL (>=3)
Version2.2.4-10

View on R-Forge

Files

GWAtoolbox/COPYING
GWAtoolbox/DESCRIPTION
GWAtoolbox/NAMESPACE
GWAtoolbox/R
GWAtoolbox/R/ANNOTATE.R
GWAtoolbox/R/DISPERSION_CHECK.R
GWAtoolbox/R/GWASFORMAT.R
GWAtoolbox/R/GWASQC.R
GWAtoolbox/R/HARMONIZE.R
GWAtoolbox/R/HARMONIZE_BY_POS.R
GWAtoolbox/R/INDEPENDENT_SNPS.R
GWAtoolbox/R/KUSK_CHECK.R
GWAtoolbox/R/PANNOTATE.R
GWAtoolbox/R/PGWASFORMAT.R
GWAtoolbox/R/PGWASQC.R
GWAtoolbox/R/PLOT.R
GWAtoolbox/R/PLOT_COMBINED_BOXPLOTS.R
GWAtoolbox/R/RE.R
GWAtoolbox/inst
GWAtoolbox/inst/doc
GWAtoolbox/inst/doc/ANNOTATE_script.txt
GWAtoolbox/inst/doc/GWASFORMAT_script.txt
GWAtoolbox/inst/doc/GWASQC_script.txt
GWAtoolbox/inst/doc/GWAtoolbox.Rnw
GWAtoolbox/inst/doc/GWAtoolbox.pdf
GWAtoolbox/inst/doc/PANNOTATE_script.txt
GWAtoolbox/inst/doc/PGWASFORMAT_script.txt
GWAtoolbox/inst/doc/PGWASQC_script.txt
GWAtoolbox/inst/doc/dispersion.png
GWAtoolbox/inst/doc/genes_HGNC_ensembl_rel54_may2009_b36.txt
GWAtoolbox/inst/doc/genes_HGNC_ensembl_rel67_may2012_b37.txt
GWAtoolbox/inst/doc/gwa_data_example_1.txt
GWAtoolbox/inst/doc/gwa_data_example_2.tbl
GWAtoolbox/inst/doc/gwa_data_example_3.csv
GWAtoolbox/inst/doc/gwa_data_example_4.txt
GWAtoolbox/inst/doc/gwa_data_example_5.csv
GWAtoolbox/inst/doc/kusk_check.png
GWAtoolbox/inst/doc/map_b37.txt
GWAtoolbox/inst/doc/plots.png
GWAtoolbox/inst/doc/workflow.png
GWAtoolbox/inst/extdata
GWAtoolbox/inst/extdata/content_style.css
GWAtoolbox/inst/extdata/menu_style.css
GWAtoolbox/inst/extdata/script.js
GWAtoolbox/man
GWAtoolbox/man/annotate.Rd GWAtoolbox/man/dispersion_check.Rd GWAtoolbox/man/gwasformat.Rd GWAtoolbox/man/gwasqc.Rd GWAtoolbox/man/harmonize.Rd GWAtoolbox/man/harmonize_by_pos.Rd GWAtoolbox/man/independent_snps.Rd GWAtoolbox/man/kusk_check.Rd GWAtoolbox/man/pannotate.Rd GWAtoolbox/man/pgwasformat.Rd GWAtoolbox/man/pgwasqc.Rd GWAtoolbox/man/re.Rd
GWAtoolbox/src
GWAtoolbox/src/GWAtoolbox.cpp
GWAtoolbox/src/GWAtoolbox.h
GWAtoolbox/src/Makevars
GWAtoolbox/src/Makevars.win
GWAtoolbox/src/annotation
GWAtoolbox/src/annotation/Annotator.cpp
GWAtoolbox/src/annotation/AnnotatorException.cpp
GWAtoolbox/src/annotation/Makefile
GWAtoolbox/src/annotation/include
GWAtoolbox/src/annotation/include/Annotator.h
GWAtoolbox/src/annotation/include/AnnotatorException.h
GWAtoolbox/src/auxiliary
GWAtoolbox/src/auxiliary/Makefile
GWAtoolbox/src/auxiliary/auxiliary.cpp
GWAtoolbox/src/auxiliary/include
GWAtoolbox/src/auxiliary/include/auxiliary.h
GWAtoolbox/src/bitarray
GWAtoolbox/src/bitarray/BitArray.cpp
GWAtoolbox/src/bitarray/BitArrayException.cpp
GWAtoolbox/src/bitarray/Makefile
GWAtoolbox/src/bitarray/include
GWAtoolbox/src/bitarray/include/BitArray.h
GWAtoolbox/src/bitarray/include/BitArrayException.h
GWAtoolbox/src/descriptor
GWAtoolbox/src/descriptor/Descriptor.cpp
GWAtoolbox/src/descriptor/DescriptorException.cpp
GWAtoolbox/src/descriptor/Makefile
GWAtoolbox/src/descriptor/include
GWAtoolbox/src/descriptor/include/Descriptor.h
GWAtoolbox/src/descriptor/include/DescriptorException.h
GWAtoolbox/src/exception
GWAtoolbox/src/exception/Exception.cpp
GWAtoolbox/src/exception/Makefile
GWAtoolbox/src/exception/include
GWAtoolbox/src/exception/include/Exception.h
GWAtoolbox/src/gwafile
GWAtoolbox/src/gwafile/GwaFile.cpp
GWAtoolbox/src/gwafile/GwaFileException.cpp
GWAtoolbox/src/gwafile/Makefile
GWAtoolbox/src/gwafile/include
GWAtoolbox/src/gwafile/include/GwaFile.h
GWAtoolbox/src/gwafile/include/GwaFileException.h
GWAtoolbox/src/gwasformat
GWAtoolbox/src/gwasformat/include
GWAtoolbox/src/gwasformat/include/columns
GWAtoolbox/src/gwasformat/include/columns/Column.h
GWAtoolbox/src/gwasformat/include/columns/ColumnException.h
GWAtoolbox/src/gwasformat/include/columns/CorrectedPvalueColumn.h
GWAtoolbox/src/gwasformat/include/columns/CorrectedStandardErrorColumn.h
GWAtoolbox/src/gwasformat/include/columns/EffectiveSampleSizeColumn.h
GWAtoolbox/src/gwasformat/include/formatter
GWAtoolbox/src/gwasformat/include/formatter/Formatter.h
GWAtoolbox/src/gwasformat/include/formatter/FormatterException.h
GWAtoolbox/src/gwasformat/libs
GWAtoolbox/src/gwasformat/libs/columns
GWAtoolbox/src/gwasformat/libs/columns/Column.cpp
GWAtoolbox/src/gwasformat/libs/columns/ColumnException.cpp
GWAtoolbox/src/gwasformat/libs/columns/CorrectedPvalueColumn.cpp
GWAtoolbox/src/gwasformat/libs/columns/CorrectedStandardErrorColumn.cpp
GWAtoolbox/src/gwasformat/libs/columns/EffectiveSampleSizeColumn.cpp
GWAtoolbox/src/gwasformat/libs/columns/Makefile
GWAtoolbox/src/gwasformat/libs/formatter
GWAtoolbox/src/gwasformat/libs/formatter/Formatter.cpp
GWAtoolbox/src/gwasformat/libs/formatter/FormatterException.cpp
GWAtoolbox/src/gwasformat/libs/formatter/Makefile
GWAtoolbox/src/gwasqc
GWAtoolbox/src/gwasqc/include
GWAtoolbox/src/gwasqc/include/analyzer
GWAtoolbox/src/gwasqc/include/analyzer/Analyzer.h
GWAtoolbox/src/gwasqc/include/analyzer/AnalyzerException.h
GWAtoolbox/src/gwasqc/include/expressions
GWAtoolbox/src/gwasqc/include/expressions/Conjunction.h
GWAtoolbox/src/gwasqc/include/expressions/Disjunction.h
GWAtoolbox/src/gwasqc/include/expressions/Evaluable.h
GWAtoolbox/src/gwasqc/include/expressions/Get.h
GWAtoolbox/src/gwasqc/include/expressions/Gt.h
GWAtoolbox/src/gwasqc/include/expressions/Let.h
GWAtoolbox/src/gwasqc/include/expressions/Lt.h
GWAtoolbox/src/gwasqc/include/metas
GWAtoolbox/src/gwasqc/include/metas/Meta.h
GWAtoolbox/src/gwasqc/include/metas/MetaCrossTable.h
GWAtoolbox/src/gwasqc/include/metas/MetaException.h
GWAtoolbox/src/gwasqc/include/metas/MetaFiltered.h
GWAtoolbox/src/gwasqc/include/metas/MetaFormat.h
GWAtoolbox/src/gwasqc/include/metas/MetaGroup.h
GWAtoolbox/src/gwasqc/include/metas/MetaImplausible.h
GWAtoolbox/src/gwasqc/include/metas/MetaImplausibleStrict.h
GWAtoolbox/src/gwasqc/include/metas/MetaImplausibleStrictAdjusted.h
GWAtoolbox/src/gwasqc/include/metas/MetaNumeric.h
GWAtoolbox/src/gwasqc/include/metas/MetaRatio.h
GWAtoolbox/src/gwasqc/include/metas/MetaUniqueness.h
GWAtoolbox/src/gwasqc/include/plots
GWAtoolbox/src/gwasqc/include/plots/Boxplot.h
GWAtoolbox/src/gwasqc/include/plots/Histogram.h
GWAtoolbox/src/gwasqc/include/plots/Plot.h
GWAtoolbox/src/gwasqc/include/plots/PlotException.h
GWAtoolbox/src/gwasqc/include/plots/Plottable.h
GWAtoolbox/src/gwasqc/include/plots/Qqplot.h
GWAtoolbox/src/gwasqc/libs
GWAtoolbox/src/gwasqc/libs/analyzer
GWAtoolbox/src/gwasqc/libs/analyzer/Analyzer.cpp
GWAtoolbox/src/gwasqc/libs/analyzer/AnalyzerException.cpp
GWAtoolbox/src/gwasqc/libs/analyzer/Makefile
GWAtoolbox/src/gwasqc/libs/expressions
GWAtoolbox/src/gwasqc/libs/expressions/Conjunction.cpp
GWAtoolbox/src/gwasqc/libs/expressions/Disjunction.cpp
GWAtoolbox/src/gwasqc/libs/expressions/Evaluable.cpp
GWAtoolbox/src/gwasqc/libs/expressions/Get.cpp
GWAtoolbox/src/gwasqc/libs/expressions/Gt.cpp
GWAtoolbox/src/gwasqc/libs/expressions/Let.cpp
GWAtoolbox/src/gwasqc/libs/expressions/Lt.cpp
GWAtoolbox/src/gwasqc/libs/expressions/Makefile
GWAtoolbox/src/gwasqc/libs/metas
GWAtoolbox/src/gwasqc/libs/metas/Makefile
GWAtoolbox/src/gwasqc/libs/metas/Meta.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaCrossTable.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaException.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaFiltered.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaFormat.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaGroup.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaImplausible.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaImplausibleStrict.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaImplausibleStrictAdjusted.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaNumeric.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaRatio.cpp
GWAtoolbox/src/gwasqc/libs/metas/MetaUniqueness.cpp
GWAtoolbox/src/gwasqc/libs/plots
GWAtoolbox/src/gwasqc/libs/plots/Boxplot.cpp
GWAtoolbox/src/gwasqc/libs/plots/Histogram.cpp
GWAtoolbox/src/gwasqc/libs/plots/Makefile
GWAtoolbox/src/gwasqc/libs/plots/Plot.cpp
GWAtoolbox/src/gwasqc/libs/plots/PlotException.cpp
GWAtoolbox/src/gwasqc/libs/plots/Qqplot.cpp
GWAtoolbox/src/harmonization
GWAtoolbox/src/harmonization/Harmonizer.cpp
GWAtoolbox/src/harmonization/Harmonizer2.cpp
GWAtoolbox/src/harmonization/Harmonizer2Exception.cpp
GWAtoolbox/src/harmonization/Harmonizer2Log.cpp
GWAtoolbox/src/harmonization/HarmonizerException.cpp
GWAtoolbox/src/harmonization/Makefile
GWAtoolbox/src/harmonization/include
GWAtoolbox/src/harmonization/include/Harmonizer.h
GWAtoolbox/src/harmonization/include/Harmonizer2.h
GWAtoolbox/src/harmonization/include/Harmonizer2Exception.h
GWAtoolbox/src/harmonization/include/Harmonizer2Log.h
GWAtoolbox/src/harmonization/include/HarmonizerException.h
GWAtoolbox/src/independization
GWAtoolbox/src/independization/Makefile
GWAtoolbox/src/independization/Selector.cpp
GWAtoolbox/src/independization/SelectorException.cpp
GWAtoolbox/src/independization/include
GWAtoolbox/src/independization/include/Selector.h
GWAtoolbox/src/independization/include/SelectorException.h
GWAtoolbox/src/intervaltree
GWAtoolbox/src/intervaltree/Interval.cpp
GWAtoolbox/src/intervaltree/IntervalTree.cpp
GWAtoolbox/src/intervaltree/Makefile
GWAtoolbox/src/intervaltree/include
GWAtoolbox/src/intervaltree/include/Interval.h
GWAtoolbox/src/intervaltree/include/IntervalTree.h
GWAtoolbox/src/randomeffect
GWAtoolbox/src/randomeffect/Makefile
GWAtoolbox/src/randomeffect/Sampler.cpp
GWAtoolbox/src/randomeffect/SamplerException.cpp
GWAtoolbox/src/randomeffect/include
GWAtoolbox/src/randomeffect/include/Sampler.h
GWAtoolbox/src/randomeffect/include/SamplerException.h
GWAtoolbox/src/reader
GWAtoolbox/src/reader/GzipReader.cpp
GWAtoolbox/src/reader/Makefile
GWAtoolbox/src/reader/Reader.cpp
GWAtoolbox/src/reader/ReaderException.cpp
GWAtoolbox/src/reader/ReaderFactory.cpp
GWAtoolbox/src/reader/TextReader.cpp
GWAtoolbox/src/reader/include
GWAtoolbox/src/reader/include/GzipReader.h
GWAtoolbox/src/reader/include/Reader.h
GWAtoolbox/src/reader/include/ReaderException.h
GWAtoolbox/src/reader/include/ReaderFactory.h
GWAtoolbox/src/reader/include/TextReader.h
GWAtoolbox/src/writer
GWAtoolbox/src/writer/GzipWriter.cpp
GWAtoolbox/src/writer/Makefile
GWAtoolbox/src/writer/TextWriter.cpp
GWAtoolbox/src/writer/Writer.cpp
GWAtoolbox/src/writer/WriterException.cpp
GWAtoolbox/src/writer/WriterFactory.cpp
GWAtoolbox/src/writer/include
GWAtoolbox/src/writer/include/GzipWriter.h
GWAtoolbox/src/writer/include/TextWriter.h
GWAtoolbox/src/writer/include/Writer.h
GWAtoolbox/src/writer/include/WriterException.h
GWAtoolbox/src/writer/include/WriterFactory.h
GWAtoolbox/src/zlib
GWAtoolbox/src/zlib/Makefile
GWAtoolbox/src/zlib/adler32.c
GWAtoolbox/src/zlib/compress.c
GWAtoolbox/src/zlib/crc32.c
GWAtoolbox/src/zlib/crc32.h
GWAtoolbox/src/zlib/deflate.c
GWAtoolbox/src/zlib/deflate.h
GWAtoolbox/src/zlib/gzclose.c
GWAtoolbox/src/zlib/gzguts.h
GWAtoolbox/src/zlib/gzlib.c
GWAtoolbox/src/zlib/gzread.c
GWAtoolbox/src/zlib/gzwrite.c
GWAtoolbox/src/zlib/infback.c
GWAtoolbox/src/zlib/inffast.c
GWAtoolbox/src/zlib/inffast.h
GWAtoolbox/src/zlib/inffixed.h
GWAtoolbox/src/zlib/inflate.c
GWAtoolbox/src/zlib/inflate.h
GWAtoolbox/src/zlib/inftrees.c
GWAtoolbox/src/zlib/inftrees.h
GWAtoolbox/src/zlib/trees.c
GWAtoolbox/src/zlib/trees.h
GWAtoolbox/src/zlib/uncompr.c
GWAtoolbox/src/zlib/zconf.h
GWAtoolbox/src/zlib/zlib.h
GWAtoolbox/src/zlib/zutil.c
GWAtoolbox/src/zlib/zutil.h

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