In aneuraz/multimodalPhewas: multiWAS

# The `params` object is available in the document.
knitr::opts_chunk$set(echo = FALSE)
knitr::opts_chunk$set(warning = FALSE)
knitr::opts_chunk$set(message = FALSE)
params$n
library(ggplot2)
library(plotly)
library(DT)

Cohortes

Cases : r params$cases

Controls : r params$controls

Description of the population

DT::datatable(params$patients)

if (!is.na(params$manhattan_concepts)) {

  cat('## UMLS concepts from narrative reports\n\n')

  cat('### Manhattan plot\n\n')
}

if(!is.na(params$manhattan_concepts))  params$manhattan_concepts

if (!is.na(params$manhattan_concepts)) {

  cat('### Result table\n\n')

}

if(!is.na(params$table_concepts)) DT::datatable(params$table_concepts)

if (!is.na(params$dumbbell_concepts)) {

  cat('### Dumbbell plot of bootstrapped ORs\n\n')
}

if(!is.na(params$dumbbell_concepts)) params$dumbbell_concepts

if (!is.na(params$dumbbell_concepts)) {

  cat('### Dumbbell plot of bootstrapped ORs\n\n')
}

if(!is.na(params$dumbbell_concepts)) params$dumbbell_concepts

if (!is.na(params$manhattan_bio)) {

  cat('## Biological test results\n\n')

  cat('### Manhattan plot\n\n')
}

if(!is.na(params$manhattan_bio)) params$manhattan_bio

if (!is.na(params$table_bio)) {

  cat('### Result table\n\n')

}

if(!is.na(params$table_bio)) DT::datatable(params$table_bio)

if (!is.na(params$dumbbell_bio)) {

  cat('### Dumbbell plot of bootstrapped ORs\n\n')
}

if(!is.na(params$dumbbell_bio)) params$dumbbell_bio

if (!is.na(params$manhattan_cim)) {

  cat('## ICD codes\n\n')

  cat('### Manhattan plot\n\n')
}

if(!is.na(params$manhattan_cim)) params$manhattan_cim

if (!is.na(params$table_cim)) {

  cat('### Result table\n\n')

}

if(!is.na(params$table_cim)) DT::datatable(params$table_cim)

if (!is.na(params$dumbbell_cim)) {

  cat('### Dumbbell plot of bootstrapped ORs\n\n')
}

if(!is.na(params$dumbbell_cim)) params$dumbbell_cim

aneuraz/multimodalPhewas documentation built on May 29, 2019, 4:50 p.m.