cotsapas_data: Summary Statistics from "Pervasive Sharing of Genetic Effects...

In trochet/metabf: Meta-analysis of Genome-wide Association Studies Using Approximate Bayes Factors

Description

Summary statistics from seven genome-wide association studies, which were used in “Pervasive Sharing of Genetic Effects in Autoimmune Disease” by Cotsapas et. al. (see reference below). This dataset is meant to be used in demonstrations of the metabf package.

Usage

cotsapas

Format

A data frame with the summary statistics for seven autoimmune diseases across 107 single nucleotide polymorphisms. The columns are described below.

SNP

The rsid of the single nucleotide polymorphism (SNP).

CHR

The chromosome where the SNP is located.

POS

The basepair position of the SNP on the chromosome.

major_al

The major allele of the SNP.

minor_al

The minor allele of the SNP.

freq

The frequency of the minor allele.

RA.

Values with this prefix pertain to data from a genome-wide associiation study of rheumatoid arthritis.

PS.

Values with this prefix pertain to data from a genome-wide associiation study of psoriasis.

MS.

Values with this prefix pertain to data from a genome-wide associiation study of multiple sclerosis.

SLE.

Values with this prefix pertain to data from a genome-wide associiation study of systemic lupus erythematosus.

CD.

Values with this prefix pertain to data from a genome-wide associiation study of Crohn's disease.

CeD.

Values with this prefix pertain to data from a genome-wide associiation study of coeliac disease.

T1D.

Values with this prefix pertain to data from a genome-wide associiation study of type 1 diabetes.

.beta

Values with this suffix show the effect size estimate (or log of the odds ratio) of the SNP on the disease.

.SE

Values with this suffix show the standard error of the effect size estimate of the SNP on the disease.

.P

Values with this suffix show the p-value of the effect of SNP on the disease.

Details

These data come from studies collated by Cotsapas et al. (see References below). The original paper listed Z-scores and p-values. We have used 1000 Genomes and the individual study sizes to estimate the standard errors and from that, the effect sizes. The listed SNP positions have also been update to match GRCh37.

Source

Dataset S1 from “Pervasive Sharing of Genetic Effects in Autoimmune Disease”. (See reference below)

References

Cotsapas C, Voight BF, Rossin E, Lage K, Neale BM, Wallace C, et al. (2011) Pervasive Sharing of Genetic Effects in Autoimmune Disease. PLoS Genetics 7(8): e1002254. doi:10.1371/journal.pgen.1002254

The 1000 Genomes Projet Consortium. (2015) A global reference for human genetic variation. Nature 526, 68–74. doi:10.1038/nature15393

Examples

cotsapas[1:10,]
names(cotsapas)

#To obtain all the effect size estimates
betas <- cotsapas[,grep("\\.beta", names(cotsapas))]

trochet/metabf documentation built on Nov. 9, 2021, 1:08 p.m.