gwa_sample {QCGWAS}

Sample dataset for the QCGWAS package

Description

A fake GWAS results dataset for use in the examples.

Usage

data(gwa_sample)

Format

A data frame with 10000 observations on the following 15 variables.

MARKER

a character vector; the SNP IDs.

STRAND

a character vector; the DNA strand of the listed alleles.

CHR

a character vector; the chromosome of the listed SNP.

POSITION

a numeric vector; the basepair position of the listed SNP.

EFFECT_ALL

a character vector; the effect allele.

OTHER_ALL

a character vector; the non-effect allele.

N_TOTAL

a numeric vector; the sample size.

EFF_ALL_FREQ

a numeric vector; frequency of the effect-allele in the dataset.

HWE_PVAL

a numeric vector; Hardy-Weinberg (HWE) p-value of the listed alleles.

CALLRATE

a numeric vector; SNP callrate.

EFFECT

a numeric vector; effect size of the listed effect allele.

STDERR

a numeric vector; standard error of the effect.

PVALUE

a numeric vector; p-value of the effect.

IMPUTED

a numeric vector; imputation status - i.e. whether the SNP is genotyped (0) or imputed (1).

IMP_QUALITY

a numeric vector; imputation quality.