QCGWAS: Quality Control of Genome Wide Association Study results

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Tools for (automated and manual) quality control of the results of Genome Wide Association Studies

Author
Peter J. van der Most and Ilja M. Nolte
Date of publication
2014-02-12 14:42:16
Maintainer
Peter J. van der Most <p.j.van.der.most@umcg.nl>
License
GPL (>= 3)
Version
1.0-8

View on CRAN

Man pages

calc_kurtosis
Skewness and Kurtosis
check_P
Checking GWAS p-values
convert_impstatus
Convert imputation-status values to the QCGWAS standard
create_hapmap_reference
Create an allele-reference file from HapMap data
filter_GWAS
Automated filtering and reformatting of GWAS results files
gwa_sample
Sample dataset for the QCGWAS package
header_translations
Translation table for GWAS dataset headers
HQ_filter
Select high-quality data in GWAS datasets
identify_column
Identify non-standard column names
intensity_plot
Generates an intensity plot from x, y datasets
load_GWAS
Easy loading of GWAS results files
match_alleles
Check and correct alleles in GWAS result files
plot_distribution
GWAS effect-Size distribution plot
plot_precision
GWAS Precision Plot
plot_regional
Regional Association Plot
plot_skewness
GWAS Skewness vs. Kurtosis Plot
QC_GWAS
Automated Quality Control of GWAS Results files
QCGWAS-package
Quality Control of Genome Wide Association Study results
QC_histogram
Histogram(s) of expected and observed data distribution
QC_plots
QQ and Manhattan plots
QQ_plot
QQ plot(s) of expected vs. reported p-values
save_log
Log entries for QC_GWAS
switch_strand
Convert alleles to the opposing DNA strand
translate_header
Translate column names into standard names

Files in this package

QCGWAS
QCGWAS/inst
QCGWAS/inst/CITATION
QCGWAS/inst/doc
QCGWAS/inst/doc/QCGWAS_v10-8_documentation.doc
QCGWAS/inst/doc/QCGWAS_v10_8_manual.pdf
QCGWAS/inst/doc/QCGWAS_v10-8_quick_start_guide.doc
QCGWAS/inst/doc/header_translations.txt
QCGWAS/NAMESPACE
QCGWAS/data
QCGWAS/data/gwa_sample.rda
QCGWAS/data/header_translations.rda
QCGWAS/R
QCGWAS/R/QC_plots.R
QCGWAS/R/plot_precision.R
QCGWAS/R/calc_skewness.R
QCGWAS/R/check_P.R
QCGWAS/R/QQ_series.R
QCGWAS/R/translate_header.R
QCGWAS/R/plot_regional.R
QCGWAS/R/convert_impstatus.R
QCGWAS/R/QQ_plot.R
QCGWAS/R/HQ_filter.R
QCGWAS/R/switch_strand.R
QCGWAS/R/plot_skewness.R
QCGWAS/R/QC_series.R
QCGWAS/R/QCGWAS-internal.R
QCGWAS/R/calc_kurtosis.R
QCGWAS/R/load_test.R
QCGWAS/R/histogram_series.R
QCGWAS/R/match_alleles.R
QCGWAS/R/QC_GWAS.R
QCGWAS/R/plot_distribution.R
QCGWAS/R/identify_column.R
QCGWAS/R/save_log.R
QCGWAS/R/load_GWAS.R
QCGWAS/R/filter_GWAS.R
QCGWAS/R/create_hapmap_reference.R
QCGWAS/R/QC_histogram.R
QCGWAS/R/intensity_plot.R
QCGWAS/MD5
QCGWAS/DESCRIPTION
QCGWAS/man
QCGWAS/man/QC_histogram.Rd
QCGWAS/man/HQ_filter.Rd
QCGWAS/man/QQ_plot.Rd
QCGWAS/man/plot_regional.Rd
QCGWAS/man/convert_impstatus.Rd
QCGWAS/man/plot_skewness.Rd
QCGWAS/man/check_P.Rd
QCGWAS/man/plot_distribution.Rd
QCGWAS/man/plot_precision.Rd
QCGWAS/man/QC_plots.Rd
QCGWAS/man/save_log.Rd
QCGWAS/man/QCGWAS-package.Rd
QCGWAS/man/load_GWAS.Rd
QCGWAS/man/translate_header.Rd
QCGWAS/man/match_alleles.Rd
QCGWAS/man/filter_GWAS.Rd
QCGWAS/man/create_hapmap_reference.Rd
QCGWAS/man/gwa_sample.Rd
QCGWAS/man/calc_kurtosis.Rd
QCGWAS/man/QC_GWAS.Rd
QCGWAS/man/header_translations.Rd
QCGWAS/man/switch_strand.Rd
QCGWAS/man/identify_column.Rd
QCGWAS/man/intensity_plot.Rd