QCGWAS (version 1.0-9)

Quality Control of Genome Wide Association Study Results

Description

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

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Version

Install

install.packages('QCGWAS')

Monthly Downloads

217

Version

1.0-9

License

GPL (>= 3)

Maintainer

Peter J van der Most

Last Published

May 30th, 2022

Functions in QCGWAS (1.0-9)

create_hapmap_reference

Create an allele-reference file from HapMap data

convert_impstatus

Convert imputation-status values to the QCGWAS standard

HQ_filter

Select high-quality data in GWAS datasets

QCGWAS-package

Quality Control of Genome Wide Association Study Results

match_alleles

Check and correct alleles in GWAS result files

QC_plots

QQ and Manhattan plots

plot_distribution

GWAS effect-Size distribution plot

load_GWAS

Easy loading of GWAS results files

intensity_plot

Generates an intensity plot from x, y datasets

check_P

Checking GWAS p-values

calc_kurtosis

Skewness and Kurtosis

identify_column

Identify non-standard column names

header_translations

Translation table for GWAS dataset headers

QC_GWAS

Automated Quality Control of GWAS Results files

gwa_sample

Sample dataset for the QCGWAS package

filter_GWAS

Automated filtering and reformatting of GWAS results files

QQ_plot

QQ plot(s) of expected vs. reported p-values

save_log

Log entries for QC_GWAS

plot_skewness

GWAS Skewness vs. Kurtosis Plot

switch_strand

Convert alleles to the opposing DNA strand

plot_precision

GWAS Precision Plot

translate_header

Translate column names into standard names

QC_histogram

Histogram(s) of expected and observed data distribution

plot_regional

Regional Association Plot