Quality Control of Genome Wide Association Study Results

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Documentation for package ‘QCGWAS’ version 1.0-9

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

QCGWAS-package	Quality Control of Genome Wide Association Study Results
calc_kurtosis	Skewness and Kurtosis
calc_skewness	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
histogram_series	Histogram(s) of expected and observed data distribution
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
load_test	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
QCGWAS	Quality Control of Genome Wide Association Study Results
QC_GWAS	Automated Quality Control of GWAS Results files
QC_histogram	Histogram(s) of expected and observed data distribution
QC_plots	QQ and Manhattan plots
QC_series	Automated Quality Control of GWAS Results files
QQ_plot	QQ plot(s) of expected vs. reported p-values
QQ_series	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