preprocess: Preprocess Multi-trait Summary Statistics

In gqi/hipo: Heritability Informed Power Optimization (HIPO)

Description

Preprocesses summary statistics for HIPO analysis. Performs SNP filtering and allele merge.

Usage

preprocess(sumstats, maf.thr = 0.05)

Arguments

sumstats

A list of K containing summary statistics for K traits. Each element is a data frame that contains at least 6 columns<ef><bc><9a>rsid, A1 (effect allele), A2, N (sample size), z (z-statistic), pval. Three optional columns can be provided: chr (chromosome number), bp (base pair; physical position), freqA1 (allele frequency of A1); if provided, SNP filtering will be applied: (1) remove MHC region (26-34Mb of chromosome 6) (2) remove variants with MAF < maf.thr (see below for maf.thr).

maf.thr

MAF threshold for quality control. SNPs with MAF < maf.thr are removed. Default 0.05, constrained between 0 and 0.5. Only effective when freqA1 is present in sumstats.

Value

A list that contains

sumstats.all	A data.frame containing the summary statistics of all individual traits.
traitvec	A vector containing the trait names.

gqi/hipo documentation built on May 18, 2019, 8:12 p.m.