PGC3 Schizophrenia Z-scores, Genome-wide — PGC3_SCZ_ilmn1M

Association Z-scores for 791,425 variants across chromosomes 1-22, from the Psychiatric Genomics Consortium's third schizophrenia GWAS wave (PGC SCZ3), restricted to variants measured on the Illumina 1M array.

Usage

data(PGC3_SCZ_ilmn1M_Z)

Format

A data.frame with 791,425 rows and 6 columns:

rsid: dbSNP rs identifier.
chr: Chromosome, 1-22.
bp: Base pair position.
a1: Reference allele.
a2: Alternative allele.
z: Association Z-score.

Details

This is the example input for fiqt, whose FDR inverse quantile transformation corrects Winner's Curse bias and therefore needs a genome-wide set of Z-scores rather than one region.

References

Trubetskoy V, Pardinas AF, Qi T, et al. (2022). Mapping genomic loci implicates genes and synaptic biology in schizophrenia. Nature 604(7906):502-508. doi:10.1038/s41586-022-04434-5

Examples

if (FALSE) { # \dontrun{
data(PGC3_SCZ_ilmn1M_Z)
str(PGC3_SCZ_ilmn1M_Z)
} # }