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mr.mtrobin's Introduction

Mr.MtRobin: Multi-tissue transcriptome-wide Mendelian Randomization method ROBust to INvalid instrumental variables

The goal of Mr.MtRobin is to provide tools to conduct transcriptome-wide Mendelian randomization analysis using the MR-MtRobin algorithm. MR-MtRobin is a Multi-tissue transcriptome-wide Mendelian Randomization method ROBust to INvalid instrumental variables that takes summary statistics from complex trait GWAS and multi-tissue eQTL analyses as input and uses a reverse regression random slope mixed model to infer whether a gene is associated with a complex trait.

Setup

To install and load functions from Mr.MtRobin, run the following:

devtools::install_github("kjgleason/Mr.MtRobin")
library("Mr.MtRobin")

Citation

To cite Mr.MtRobin in publications, please use:

Kevin J. Gleason, Fan Yang and Lin S. Chen. A robust two-sample transcriptome-wide Mendelian randomization method integrating GWAS with multi-tissue eQTL summary statistics. Genet Epidemiol (2021); 45(4):353-371. doi:10.1002/gepi.22380.

mr.mtrobin's People

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mr.mtrobin's Issues

Merge issue

Hi there,
I have been trying to play around with the examples pre-installed with your package. However, I get a merge table error every time I try running the MR_MtRobin function? Can you please help? Here is the snapshot:

IV_gene1=select_IV(geneID="gene1", eqtl_data=eqtl_stats_example, nTiss=10, LD=LD_example)

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)

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)
Error: 'merge' is not an exported object from 'namespace:data.table'

  • Session info -----------------------------------------------------------------------------------------
    setting value
    version R version 4.1.1 (2021-08-10)
    os Windows 10 x64
    system x86_64, mingw32
    ui RStudio
    language (EN)
    collate English_United Kingdom.1252
    ctype English_United Kingdom.1252
    tz Europe/London
    date 2021-08-31

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