Package: QCGWAS 1.0-9

QCGWAS: Quality Control of Genome Wide Association Study Results

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

Authors:Peter J. van der Most and Ilja M. Nolte

# Install 'QCGWAS' in R:

install.packages('QCGWAS', repos = c('https://mostpj.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

Last updated 2 years agofrom:bb665efc92. Checks:OK: 7. Indexed: yes.

Dependencies:

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