Test file for MR-TRYX

library(knitr)
knitr::opts_chunk$set(echo=TRUE, message=FALSE, warning=FALSE, dev="png", cache=TRUE, eval=FALSE)

Test commands for each function

library(TwoSampleMR)
library(MRInstruments)
library(RadialMR)
library(tryx)

Data preparation

Example: systolic blood pressure and coronary artery disease

ao <- available_outcomes()
bmi <- extract_instruments(outcomes = 2)
sbp <-  extract_outcome_data(snps=bmi$SNP, outcomes = "UKB-a:360")
dat <- harmonise_data(bmi, sbp)

Scan

Test “tryx.scan”

scan_bmi <- tryx.scan(dat)
load("~/tryx/tests/test_mrtryx.RData")

Test “tryx.sig”"

scan_bmi <- tryx.sig(scan_bmi)

Test “tryx.adjustment”

id_remove <- c(2, 72, 89, 90, "UKB-a:35", "UKB-a:359", "UKB-a:61", 1096, 85, 91, 93, 999)

ad <- tryx.adjustment(scan_bmi, id_remove = id_remove)

Test “tryx.adjustment.mv”

ad.mv <- tryx.adjustment.mv(scan_bmi, id_remove = id_remove)

Test “tryx.analyse”

an <- tryx.analyse(scan_bmi, id_remove = id_remove)

Test “tryx.analyse.mv”

an.mv <- tryx.analyse.mv(scan_bmi, id_remove = id_remove)

Yoonsu Cho

7 November 2019