gwa_sample: Sample dataset for the QCGWAS package
In QCGWAS: Quality Control of Genome Wide Association Study Results

gwa_sample

R Documentation

Sample dataset for the QCGWAS package

A fake GWAS results dataset for use in the examples.

data(gwa_sample)

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.