GWAtoolbox: GWAS Quality Control
Version 2.2.4-10

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

Browse man pages Browse package API and functions Browse package files

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
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("GWAtoolbox", repos="http://R-Forge.R-project.org")

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.

Functions

annotate Man page Source code
dispersion_check Man page Source code
gwasformat Man page Source code
gwasqc Man page Source code
harmonize Man page Source code
harmonize_by_pos Man page Source code
independent_snps Man page Source code
kusk_check Man page Source code
pannotate Man page Source code
pgwasformat Man page Source code
pgwasqc Man page Source code
plot Source code
plot_combined_boxplots Source code
re Man page Source code

Files

COPYING
DESCRIPTION
NAMESPACE
R
R/ANNOTATE.R
R/DISPERSION_CHECK.R
R/GWASFORMAT.R
R/GWASQC.R
R/HARMONIZE.R
R/HARMONIZE_BY_POS.R
R/INDEPENDENT_SNPS.R
R/KUSK_CHECK.R
R/PANNOTATE.R
R/PGWASFORMAT.R
R/PGWASQC.R
R/PLOT.R
R/PLOT_COMBINED_BOXPLOTS.R
R/RE.R
inst
inst/doc
inst/doc/ANNOTATE_script.txt
inst/doc/GWASFORMAT_script.txt
inst/doc/GWASQC_script.txt
inst/doc/GWAtoolbox.Rnw
inst/doc/GWAtoolbox.pdf
inst/doc/PANNOTATE_script.txt
inst/doc/PGWASFORMAT_script.txt
inst/doc/PGWASQC_script.txt
inst/doc/dispersion.png
inst/doc/genes_HGNC_ensembl_rel54_may2009_b36.txt
inst/doc/genes_HGNC_ensembl_rel67_may2012_b37.txt
inst/doc/gwa_data_example_1.txt
inst/doc/gwa_data_example_2.tbl
inst/doc/gwa_data_example_3.csv
inst/doc/gwa_data_example_4.txt
inst/doc/gwa_data_example_5.csv
inst/doc/kusk_check.png
inst/doc/map_b37.txt
inst/doc/plots.png
inst/doc/workflow.png
inst/extdata
inst/extdata/content_style.css
inst/extdata/menu_style.css
inst/extdata/script.js
man
man/annotate.Rd
man/dispersion_check.Rd
man/gwasformat.Rd
man/gwasqc.Rd
man/harmonize.Rd
man/harmonize_by_pos.Rd
man/independent_snps.Rd
man/kusk_check.Rd
man/pannotate.Rd
man/pgwasformat.Rd
man/pgwasqc.Rd
man/re.Rd
src
src/GWAtoolbox.cpp
src/GWAtoolbox.h
src/Makevars
src/Makevars.win
src/annotation
src/annotation/Annotator.cpp
src/annotation/AnnotatorException.cpp
src/annotation/Makefile
src/annotation/include
src/annotation/include/Annotator.h
src/annotation/include/AnnotatorException.h
src/auxiliary
src/auxiliary/Makefile
src/auxiliary/auxiliary.cpp
src/auxiliary/include
src/auxiliary/include/auxiliary.h
src/bitarray
src/bitarray/BitArray.cpp
src/bitarray/BitArrayException.cpp
src/bitarray/Makefile
src/bitarray/include
src/bitarray/include/BitArray.h
src/bitarray/include/BitArrayException.h
src/descriptor
src/descriptor/Descriptor.cpp
src/descriptor/DescriptorException.cpp
src/descriptor/Makefile
src/descriptor/include
src/descriptor/include/Descriptor.h
src/descriptor/include/DescriptorException.h
src/exception
src/exception/Exception.cpp
src/exception/Makefile
src/exception/include
src/exception/include/Exception.h
src/gwafile
src/gwafile/GwaFile.cpp
src/gwafile/GwaFileException.cpp
src/gwafile/Makefile
src/gwafile/include
src/gwafile/include/GwaFile.h
src/gwafile/include/GwaFileException.h
src/gwasformat
src/gwasformat/include
src/gwasformat/include/columns
src/gwasformat/include/columns/Column.h
src/gwasformat/include/columns/ColumnException.h
src/gwasformat/include/columns/CorrectedPvalueColumn.h
src/gwasformat/include/columns/CorrectedStandardErrorColumn.h
src/gwasformat/include/columns/EffectiveSampleSizeColumn.h
src/gwasformat/include/formatter
src/gwasformat/include/formatter/Formatter.h
src/gwasformat/include/formatter/FormatterException.h
src/gwasformat/libs
src/gwasformat/libs/columns
src/gwasformat/libs/columns/Column.cpp
src/gwasformat/libs/columns/ColumnException.cpp
src/gwasformat/libs/columns/CorrectedPvalueColumn.cpp
src/gwasformat/libs/columns/CorrectedStandardErrorColumn.cpp
src/gwasformat/libs/columns/EffectiveSampleSizeColumn.cpp
src/gwasformat/libs/columns/Makefile
src/gwasformat/libs/formatter
src/gwasformat/libs/formatter/Formatter.cpp
src/gwasformat/libs/formatter/FormatterException.cpp
src/gwasformat/libs/formatter/Makefile
src/gwasqc
src/gwasqc/include
src/gwasqc/include/analyzer
src/gwasqc/include/analyzer/Analyzer.h
src/gwasqc/include/analyzer/AnalyzerException.h
src/gwasqc/include/expressions
src/gwasqc/include/expressions/Conjunction.h
src/gwasqc/include/expressions/Disjunction.h
src/gwasqc/include/expressions/Evaluable.h
src/gwasqc/include/expressions/Get.h
src/gwasqc/include/expressions/Gt.h
src/gwasqc/include/expressions/Let.h
src/gwasqc/include/expressions/Lt.h
src/gwasqc/include/metas
src/gwasqc/include/metas/Meta.h
src/gwasqc/include/metas/MetaCrossTable.h
src/gwasqc/include/metas/MetaException.h
src/gwasqc/include/metas/MetaFiltered.h
src/gwasqc/include/metas/MetaFormat.h
src/gwasqc/include/metas/MetaGroup.h
src/gwasqc/include/metas/MetaImplausible.h
src/gwasqc/include/metas/MetaImplausibleStrict.h
src/gwasqc/include/metas/MetaImplausibleStrictAdjusted.h
src/gwasqc/include/metas/MetaNumeric.h
src/gwasqc/include/metas/MetaRatio.h
src/gwasqc/include/metas/MetaUniqueness.h
src/gwasqc/include/plots
src/gwasqc/include/plots/Boxplot.h
src/gwasqc/include/plots/Histogram.h
src/gwasqc/include/plots/Plot.h
src/gwasqc/include/plots/PlotException.h
src/gwasqc/include/plots/Plottable.h
src/gwasqc/include/plots/Qqplot.h
src/gwasqc/libs
src/gwasqc/libs/analyzer
src/gwasqc/libs/analyzer/Analyzer.cpp
src/gwasqc/libs/analyzer/AnalyzerException.cpp
src/gwasqc/libs/analyzer/Makefile
src/gwasqc/libs/expressions
src/gwasqc/libs/expressions/Conjunction.cpp
src/gwasqc/libs/expressions/Disjunction.cpp
src/gwasqc/libs/expressions/Evaluable.cpp
src/gwasqc/libs/expressions/Get.cpp
src/gwasqc/libs/expressions/Gt.cpp
src/gwasqc/libs/expressions/Let.cpp
src/gwasqc/libs/expressions/Lt.cpp
src/gwasqc/libs/expressions/Makefile
src/gwasqc/libs/metas
src/gwasqc/libs/metas/Makefile
src/gwasqc/libs/metas/Meta.cpp
src/gwasqc/libs/metas/MetaCrossTable.cpp
src/gwasqc/libs/metas/MetaException.cpp
src/gwasqc/libs/metas/MetaFiltered.cpp
src/gwasqc/libs/metas/MetaFormat.cpp
src/gwasqc/libs/metas/MetaGroup.cpp
src/gwasqc/libs/metas/MetaImplausible.cpp
src/gwasqc/libs/metas/MetaImplausibleStrict.cpp
src/gwasqc/libs/metas/MetaImplausibleStrictAdjusted.cpp
src/gwasqc/libs/metas/MetaNumeric.cpp
src/gwasqc/libs/metas/MetaRatio.cpp
src/gwasqc/libs/metas/MetaUniqueness.cpp
src/gwasqc/libs/plots
src/gwasqc/libs/plots/Boxplot.cpp
src/gwasqc/libs/plots/Histogram.cpp
src/gwasqc/libs/plots/Makefile
src/gwasqc/libs/plots/Plot.cpp
src/gwasqc/libs/plots/PlotException.cpp
src/gwasqc/libs/plots/Qqplot.cpp
src/harmonization
src/harmonization/Harmonizer.cpp
src/harmonization/Harmonizer2.cpp
src/harmonization/Harmonizer2Exception.cpp
src/harmonization/Harmonizer2Log.cpp
src/harmonization/HarmonizerException.cpp
src/harmonization/Makefile
src/harmonization/include
src/harmonization/include/Harmonizer.h
src/harmonization/include/Harmonizer2.h
src/harmonization/include/Harmonizer2Exception.h
src/harmonization/include/Harmonizer2Log.h
src/harmonization/include/HarmonizerException.h
src/independization
src/independization/Makefile
src/independization/Selector.cpp
src/independization/SelectorException.cpp
src/independization/include
src/independization/include/Selector.h
src/independization/include/SelectorException.h
src/intervaltree
src/intervaltree/Interval.cpp
src/intervaltree/IntervalTree.cpp
src/intervaltree/Makefile
src/intervaltree/include
src/intervaltree/include/Interval.h
src/intervaltree/include/IntervalTree.h
src/randomeffect
src/randomeffect/Makefile
src/randomeffect/Sampler.cpp
src/randomeffect/SamplerException.cpp
src/randomeffect/include
src/randomeffect/include/Sampler.h
src/randomeffect/include/SamplerException.h
src/reader
src/reader/GzipReader.cpp
src/reader/Makefile
src/reader/Reader.cpp
src/reader/ReaderException.cpp
src/reader/ReaderFactory.cpp
src/reader/TextReader.cpp
src/reader/include
src/reader/include/GzipReader.h
src/reader/include/Reader.h
src/reader/include/ReaderException.h
src/reader/include/ReaderFactory.h
src/reader/include/TextReader.h
src/writer
src/writer/GzipWriter.cpp
src/writer/Makefile
src/writer/TextWriter.cpp
src/writer/Writer.cpp
src/writer/WriterException.cpp
src/writer/WriterFactory.cpp
src/writer/include
src/writer/include/GzipWriter.h
src/writer/include/TextWriter.h
src/writer/include/Writer.h
src/writer/include/WriterException.h
src/writer/include/WriterFactory.h
src/zlib
src/zlib/Makefile
src/zlib/adler32.c
src/zlib/compress.c
src/zlib/crc32.c
src/zlib/crc32.h
src/zlib/deflate.c
src/zlib/deflate.h
src/zlib/gzclose.c
src/zlib/gzguts.h
src/zlib/gzlib.c
src/zlib/gzread.c
src/zlib/gzwrite.c
src/zlib/infback.c
src/zlib/inffast.c
src/zlib/inffast.h
src/zlib/inffixed.h
src/zlib/inflate.c
src/zlib/inflate.h
src/zlib/inftrees.c
src/zlib/inftrees.h
src/zlib/trees.c
src/zlib/trees.h
src/zlib/uncompr.c
src/zlib/zconf.h
src/zlib/zlib.h
src/zlib/zutil.c
src/zlib/zutil.h
GWAtoolbox documentation built on May 21, 2017, 12:49 a.m.