gwa_sample

A fake GWAS results dataset for use in the examples.

datasets

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

Peter J van der Most

QCGWAS

Quality Control of Genome Wide Association Study Results

gwa_sample function

A data frame with 10000 observations on the following 15 variables.<dl class="dl-horizontal">
 <dt><code>MARKER</code></dt><dd>a character vector; the SNP IDs.</dd>
 <dt><code>STRAND</code></dt><dd>a character vector; the DNA strand of
 the listed alleles.</dd>
 <dt><code>CHR</code></dt><dd>a character vector; the chromosome of the
 listed SNP.</dd>
 <dt><code>POSITION</code></dt><dd>a numeric vector; the basepair
 position of the listed SNP.</dd>
 <dt><code>EFFECT_ALL</code></dt><dd>a character vector; the effect
 allele.</dd>
 <dt><code>OTHER_ALL</code></dt><dd>a character vector; the non-effect
 allele.</dd>
 <dt><code>N_TOTAL</code></dt><dd>a numeric vector; the sample size.</dd>
 <dt><code>EFF_ALL_FREQ</code></dt><dd>a numeric vector; frequency of
 the effect-allele in the dataset.</dd>
 <dt><code>HWE_PVAL</code></dt><dd>a numeric vector; Hardy-Weinberg
 (HWE) p-value of the listed alleles.</dd>
 <dt><code>CALLRATE</code></dt><dd>a numeric vector; SNP callrate.</dd>
 <dt><code>EFFECT</code></dt><dd>a numeric vector; effect size of the
 listed effect allele.</dd>
 <dt><code>STDERR</code></dt><dd>a numeric vector; standard error of the
 effect.</dd>
 <dt><code>PVALUE</code></dt><dd>a numeric vector; p-value of the
 effect.</dd>
 <dt><code>IMPUTED</code></dt><dd>a numeric vector; imputation status -
 i.e. whether the SNP is genotyped (<code>0</code>) or imputed
 (<code>1</code>).</dd>
 <dt><code>IMP_QUALITY</code></dt><dd>a numeric vector; imputation
 quality.</dd>
 </dl>

Format

Sample dataset for the QCGWAS package — gwa_sample

A data frame with 10000 observations on the following 15 variables.<dl class='dl-horizontal'>
 <dt><code>MARKER</code></dt><dd>a character vector; the SNP IDs.</dd>
 <dt><code>STRAND</code></dt><dd>a character vector; the DNA strand of
 the listed alleles.</dd>
 <dt><code>CHR</code></dt><dd>a character vector; the chromosome of the
 listed SNP.</dd>
 <dt><code>POSITION</code></dt><dd>a numeric vector; the basepair
 position of the listed SNP.</dd>
 <dt><code>EFFECT_ALL</code></dt><dd>a character vector; the effect
 allele.</dd>
 <dt><code>OTHER_ALL</code></dt><dd>a character vector; the non-effect
 allele.</dd>
 <dt><code>N_TOTAL</code></dt><dd>a numeric vector; the sample size.</dd>
 <dt><code>EFF_ALL_FREQ</code></dt><dd>a numeric vector; frequency of
 the effect-allele in the dataset.</dd>
 <dt><code>HWE_PVAL</code></dt><dd>a numeric vector; Hardy-Weinberg
 (HWE) p-value of the listed alleles.</dd>
 <dt><code>CALLRATE</code></dt><dd>a numeric vector; SNP callrate.</dd>
 <dt><code>EFFECT</code></dt><dd>a numeric vector; effect size of the
 listed effect allele.</dd>
 <dt><code>STDERR</code></dt><dd>a numeric vector; standard error of the
 effect.</dd>
 <dt><code>PVALUE</code></dt><dd>a numeric vector; p-value of the
 effect.</dd>
 <dt><code>IMPUTED</code></dt><dd>a numeric vector; imputation status -
 i.e. whether the SNP is genotyped (<code>0</code>) or imputed
 (<code>1</code>).</dd>
 <dt><code>IMP_QUALITY</code></dt><dd>a numeric vector; imputation
 quality.</dd>
 </dl>

gwa_sample: Sample dataset for the QCGWAS package

Description

Usage

Arguments

Format