vignettes/rphg_walkthrough.R

In maize-genetics/rPHG: R front-end for the practical haplotype graph

## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(
  fig.path = "figure/graphics-",
  cache.path = "cache/graphics-",
  fig.align = "center",
  external = TRUE,
  echo = TRUE,
  warning = FALSE
)

library(rPHG)
logFile    <- tempfile(fileext = ".txt")
configFile <- tempfile()
rPHG:::createConfigFile(configFile)

## ----echo=TRUE, eval=TRUE-----------------------------------------------------
configFile |> PHGLocalCon()

## ----echo=TRUE, eval=TRUE-----------------------------------------------------
"demo.hub.maizegenetics.net" |> PHGServerCon()

## ----echo=TRUE, eval=TRUE-----------------------------------------------------
configFile |> 
    PHGLocalCon() |> 
    showPHGMethods()

## ----echo=TRUE, eval=TRUE-----------------------------------------------------
configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD")

## ----echo=TRUE, eval=TRUE-----------------------------------------------------
configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readSamples()

## ----echo=TRUE, eval=TRUE-----------------------------------------------------
configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readRefRanges()

## ----echo=TRUE, eval=TRUE-----------------------------------------------------
configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readHaplotypeIds()

## ----echo=TRUE, eval=TRUE, message=FALSE--------------------------------------
configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readPHGDataSet()