R: Quality Control of Genome Wide Association Study Results

# Quality Control of Genome Wide Association Study Results

## 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