annotateREvariance: Calculate random effect variances from annotations and...

In vafisher/AnnoRE: Random Effects Estimation for GWAS Fine Mapping with Functional Annotations

Description

Calculate random effect variances from annotations and partion of heritability.

Usage

annotateREvariance(gwas_locus, annotation, h2partition)

Arguments

gwas_locus	data frame containing GWAS summmary statistics for fine-mapping locus. Columns SNP (variant ID, any character string format), b (effect estimate), se (standard error), N (sample size), Freq1 (alternate allele frequency) are required. All SNPs are assumed to be bi-allelic.
annotation	data frame with functional annotations including the fine mapping locus. Must include columns CHR, BP, SNP, CM, and additional columns named for the annotation categories (i.e. format of ENCODE annotations at https://alkesgroup.broadinstitute.org/LDSCORE/)
h2partition	data frame with estimated heritability partition Must include column "Coefficient" with estimates, and "Category" with names of annotation categories. (i.e. format of ldsc output with –h2 option)

Value

data frame with all columns in gwas_locus plus RE variance Vbeta and its variance varVbeta. Rows represent SNPs present in both gwas_locus and annotation.

vafisher/AnnoRE documentation built on Dec. 23, 2021, 2:07 p.m.