GWAtoolbox: GWAS Quality Control

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

Author
Daniel Taliun <Daniel.Taliun@eurac.edu>, Christian Fuchsberger <cfuchsb@umich.edu>, Cristian Pattaro <Cristian.Pattaro@eurac.edu>
Date of publication
2015-05-18 20:03:20
Maintainer
Daniel Taliun <Daniel.Taliun@eurac.edu>
License
GPL (>=3)
Version
2.2.4-10

View on R-Forge

Man pages

annotate
SNPs annotation with regions (e.g. genes).
dispersion_check
Effect estimates precision by sample size.
gwasformat
Formatting of GWAS data files.
gwasqc
Quality Control Of GWA Data
harmonize
The harmonization of SNP identifiers and alleles.
harmonize_by_pos
The harmonization of SNP identifiers and alleles.
independent_snps
Selection of independent SNPs.
kusk_check
Comparison Of Skewness and Kurtosis of Effect between GWAS...
pannotate
SNPs annotation with regions (e.g. genes).
pgwasformat
Formatting of GWAS result files.
pgwasqc
Quality Control Of GWA Data
re
Random Effects Heterogeneity Analysis.

Files in this package

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