MR_MtRobin: Conduct two-sample Mendelian Randomization using summary...

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

Description

Runs the main MR-MtRobin algorithm: a Multi-Tissue transcriptome-wide Mendelian Randomization method ROBust to INvalid instrumental variables

Usage

MR_MtRobin(snpID, gwas_betas, gwas_se, eqtl_betas, eqtl_se, eqtl_pvals, LD,
  pval_thresh = 0.001)

Arguments

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).
pval_thresh	p-value threshold for instrumental variables (IVs).

Details

The following are additional details describing the input arguments. For eqtl_betas, eqtl_se, and eqtl_pvals each row i corresponds to a SNP/variant/IV while each column j holds the summary statistics in tissue type j. Both the rows of the eQTL data and the order of the GWAS vectors should match the order of snpID. 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:

lme_res	an object of class lmerMod, returned from the reverse regression random slope mixed model run by MR-MtRobin..
gwas_res	data.table of the gwas data (snpID, gwas_beta, gwas_se).
LD	matrix of LD correlation coefficients (r, not r^2).

The last two items are returned for use by MR_MtRobin_resample().

To conduct inference on the returned results, use function MR_MtRobin_resample.

Examples

## MR_MtRobin_input created using MR_MtRobin_setup()
## IV_gene1 created using select_IV()

MR_MtRobin(snpID=IV_gene1,
gwas_betas=MR_MtRobin_input$gwas_betas, gwas_se=MR_MtRobin_input$gwas_se,
eqtl_betas=MR_MtRobin_input$eqtl_betas, eqtl_se=MR_MtRobin_input$eqtl_se,
eqtl_pvals=MR_MtRobin_input$eqtl_pvals, LD=MR_MtRobin_input$LD)

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