In jwr-git/mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

knitr::opts_chunk$set(echo = F)

# Subset correct results for reporting
results <- params$report$results
results <- results[results$id.outcome == id.outcome, ]

Back to Main Page

Outcome SNPs

This table details the final list of formatted SNPs for the outcome dataset which were used in the MR analyses.

dat <- params$dat[params$dat$id.outcome == id.outcome, ]
dat[, colnames(dat) %in% c("SNP",
                           "effect_allele.outcome",
                           "other_allele.outcome",
                           "beta.outcome",
                           "eaf.outcome",
                           "chr",
                           "pos",
                           "se.outcome",
                           "pval.outcome",
                           "outcome",
                           "proxy.outcome",
                           "proxy_snp.outcome")] %>%
  dplyr::rename(Eff.Allele = effect_allele.outcome,
                Alt.Allele = other_allele.outcome,
                Beta = beta.outcome,
                EAF = eaf.outcome,
                Chr = chr,
                Pos = pos,
                SE = se.outcome,
                P.value = pval.outcome,
                Outcome = outcome,
                Proxy = proxy.outcome,
                Proxy.SNP = proxy_snp.outcome) %>%
  DT::datatable(rownames = F,
                caption = "Details for outcome SNPs, or their proxies, which were included in the MR analysis.",
                extensions = c("Buttons"),
                options = list(order = list(8, "asc"), 
                               dom = "BDfrtip", 
                               buttons = list('copy',
                                              list(extend = 'collection', 
                                                   buttons = c('csv', 'excel'), 
                                                   text = 'Download')))) %>%
  DT::formatSignif(columns = c("P.value"), digits = 3)