multiSNP: Combine LDSC, summary statistic output, and LD information...

In MichelNivard/GenomicSEM: Structural equation modeling based on GWAS summary statistics

Combine LDSC, summary statistic output, and LD information for models including multiple SNPs

Description

Function to expand the S and V matrices to include multiple SNP effects in a single matrix, along with LD information across these SNPs.

Usage

multiSNP (covstruc, SNPs, LD, SNPSE = FALSE, SNPlist = NA, ...)

Arguments

covstruc	Output from Genomic SEM multivariable LDSC
SNPs	Summary statistics file created using the sumstats function
LD	Matrix of LD information across the SNPs. If only independent SNPs are being provided a matrix of 0s can be entered. Note that the function requires that A1 and A2 be included in the LD matrix column names (e.g., rs12345_A_T)
SNPSE	User provided SE of the SNP variance for entry in the V matrix. If no number is provided the package defaults to using .0005 to reflect a practically fixed population value taken from a reference panel
SNPlist	List of rsIDs if the user wishes to subset out a set of SNPs from a full set of summary statistics

Value

The function expands the S and V matrices to include multiple SNP effects. These matrices include LD information across the SNPs.

MichelNivard/GenomicSEM documentation built on June 15, 2024, 10:41 a.m.