PGC2 Schizophrenia Allele Frequencies, Chromosome 22 — PGC2_Chr22_ilmn1M

Study reference-allele frequencies for the 13,362 chromosome 22 variants of the Psychiatric Genomics Consortium's second schizophrenia GWAS wave (PGC SCZ2) that were measured on the Illumina 1M array.

Usage

data(PGC2_Chr22_ilmn1M_AF1)

Format

A data.frame with 13,362 rows and 6 columns:

rsid: dbSNP rs identifier.
chr: Chromosome; 22 throughout.
bp: Base pair position.
a1: Reference allele.
a2: Alternative allele.
af1: Frequency of a1 in the study cohort.

Details

This is the example input for afmix, which estimates a cohort's ancestry proportions by matching its allele frequencies against the reference panel. It covers the same variants, in the same order, as PGC2_Chr22_ilmn1M_Z, and the proportions estimated from it are shipped as PGC2_SCZ_ANC_Prop.

References

Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014). Biological insights from 108 schizophrenia-associated genetic loci. Nature 511(7510):421-427. doi:10.1038/nature13595

Examples

if (FALSE) { # \dontrun{
data(PGC2_Chr22_ilmn1M_AF1)
str(PGC2_Chr22_ilmn1M_AF1)
} # }