mr.ios: MR.IOS:: Calculate index of suspicion

In universe77/mr.ios: Index of Suspicion

Description

A package for sensitivity analysis in two-samle Mendelian randomization setting when horizontal pleiotropy exists. It uses [IEU GWAS database](https://gwas.mrcieu.ac.uk/) to obtain data automatically, and is implemented to RadialMR to run the analysis.

Performs Radial inverse variance weighted (IVW) model using IOS to detect the most pleiotropic SNPs based on IOS score. The SNPs with higher score for IOS are downweighted by multiplying IOS by inverse variance weight implemented in Radial MR package.

Usage

mr.ios(
  dat = dat,
  ios = ios_dat,
  ios_type = "ios1_mean",
  alpha = 0.05,
  weights,
  tol = 1e-04
)

Arguments

dat	Harmonised dataset of the exposure and the outcome, obtained using TwoSampleMR::harmonise_data()
ios	IOS score obtained using ios()
ios_type	Types of IOS estimators. Defalt value is "ios1_mean".
alpha	Statistial significance threshold for identifying outliers. Default value is 0.05.
weights	Inverse variance weights used to calculate IVW estimate and Cochran's Q statistic, considering IOS in the model. Detailed information of the definition of each weight is provided here: https://github.com/WSpiller/RadialMR. Select first order (1), second order (2) or modified second order weights (3).
tol	Tolerance threshold for performing the iterative IVW approach. Default value is 0.0001.

Details

If a SNP influences multiple other traits then it could be 'suspicious', and more likely to be pleiotropic. This function implements two basic approaches to estimate IOS

• ios1: A summary of the SNP r2 with the other traits (r2_gu).

• ios2: A summary of the ratio of r2_gu / r2_gx, where r2_gx is the variance explained by the SNP on the exposure. Estimates the index of suspicion, whereupon SNPs which have a larger effect on a set of traits given their effect on the exposure are deemed more suspicious.

Value

List of estimates

universe77/mr.ios documentation built on Aug. 15, 2020, 9:14 a.m.