DESCRIPTION

Package: CIVMR
Title: Constrained Instrumental Variables in Mendelian Randomization with Pleiotropy
Version: 0.0.1
Authors@R: person("Lai", "Jiang", email = "jianglai1987@gmail.com", role = c("aut", "cre"))
Description: In Mendelian randomization (MR), genetic variants are used to construct instrumental variables that then enable inference about the causal
    relationship between a phenotype of interest and a response or disease outcome.
    However, valid MR inference requires several assumptions, including the
    assumption that the genetic variants only influence the response through the
    phenotype of interest.Pleiotropy occurs when a genetic variant has an effect
    on more than one different phenotypes, and therefore a pleiotropic genetic
    variant may be an invalid instrumental variable.Hence, a naive method for
    constructing an instrumental variables may lead to biased estimation of the
    association between the phenotype and the response. Here, we encode a new and
    intuitive method (Constrained Instrumental Variable method [CIV]) to construct
    valid instrumental variables and perform adjusted causal effect estimation when
    pleiotropic exists, focusing particularly on the situation where pleiotropic
    phenotypes have been measured. Our approach is theoretically guaranteed to
    perform an automatic and valid selection of genetic variants when building the
    instrumental variable. We also provide details of the features of many existing
    methods, together with a comparison of their performance in a large series of
    simulations. CIV performs robustly across many different pleiotropic violations
    of the MR assumptions.
Depends:
    R (>= 3.0.0)
Depends:
    PMA,
    plyr,
    glmnet,
    Matrix,
    foreach,
    caret,
    ggplot2,
    sem,
    MASS
License: What license is it under?
Encoding: UTF-8
LazyData: true
RoxygenNote: 5.0.1
Suggests: knitr,
    rmarkdown
VignetteBuilder: knitr