MR_MtRobin_setup: Set up data for MR-MtRobin algorithm.

In kjgleason/Mr.MtRobin: A Multi-Tissue transcriptome-wide Mendelian Randomization method ROBust to INvalid instrumental variables.

Description

Sets up data to run the main MR-MtRobin algorithm: a Multi-Tissue transcriptome-wide Mendelian Randomization method ROBust to INvalid instrumental variables.

Usage

MR_MtRobin_setup(geneID, snpID, eqtl_data, gwas_data, LD, nTiss)

Arguments

geneID	character string of the gene to be tested.
snpID	vector of variant identifiers be used as instruments for geneID.
eqtl_data	data.frame of summary statistics from eQTL study.
gwas_data	data.frame of summary statistics from GWAS study.
LD	matrix of LD correlation coefficients (r, not r^2).
nTiss	integer of the number of tissues analyzed by the eQTL study.

Details

The following are additional details describing the input arguments.

The data.frame eqtl_data should have the character variables gene_id and variant_id (as identifiers), as well as the variables beta_j, SE_j and pvalue_j for j in {1,...,nTiss}, corresponding to the coefficient, standard error, and p-value estimates from each respective eQTL analysis.

The data.frame gwas_data should have the character variable variant_id, as well as the variables beta and SE corresponding to the coefficient and standard error estimates from the GWAS analysis.

Note that the matrix LD should hold correlation coefficients (i.e. r), not their squared values (r^2).

Value

A list with the following elements:

snpID	vector of variant identifiers to be used as instrumental variables.
gwas_betas	vector of coefficient estimates (betas) from GWAS study.
gwas_se	vector of standard errors for coefficient estimates from GWAS study.
eqtl_betas	matrix of coefficient estimates (betas) from eQTL study.
eqtl_se	matrix of standard errors for coefficient estimates from eQTL study.
eqtl_pvals	matrix of p-values from eQTL study.
LD	matrix of LD correlation coefficients (r, not r^2).

The returned list elements can be passed to the main MR_MtRobin function.

Examples

MR_MtRobin_input <-
MR_MtRobin_setup(geneID="gene1",snpID=IV_gene1,eqtl_data=eqtl_stats_example,
gwas_data=gwas_stats_example,LD=LD_example,nTiss=10)

kjgleason/Mr.MtRobin documentation built on Sept. 6, 2021, 5:13 p.m.