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

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)

The basic workflow of the rPHG package is as follows:

1. Create a connection object
2. Select a PHG "method"
3. Read data into the R environment
4. Analyze and visualize data retrieval

This document introduces you to rPHG's methods and grammar, and shows you how to apply them to the previously mentioned workflow.

Creating connection objects

PHG databases can be connected through two primary sources:

• local
• server

Local connections are for databases set up to use PostgreSQL or SQLite management systems, typically located either on a local machine or hosted on a high performance compute cluster which are accessed via the PHG API.

Conversely, server connections are for databases served on publicly available web services leveraging Breeding API (BrAPI) endpoints for data retrieval. For example, demo.hub.maizegenetics.net is a publicly available PHG database housing information many known diversity populations in maize.

Establishing a local connection

To set up a local connection, prior knowledge about how configuration files are set up is needed. If you would like more information about this topic, please see the vignette "Overview of configuration files"

We can supply a path to a valid configuration file to the constructor, PHGLocalCon():

configFile |> PHGLocalCon()

Here, our configuration file path (configFilePath) is parsed to create an object of type PHGLocalCon.

Establishing a server connection

If you would like to use a PHG web service, we can use the following similar method:

"phg.maizegdb.org" |> PHGServerCon()

Here, a URL pointing to a PHG web service is supplied to the constructor PHGServerCon() which will be parsed to create an object of type PHGServerCon.

PHG Methods

configFile |> 
    PHGLocalCon() |> 
    showPHGMethods()

configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD")

Reading data

Read samples (e.g. taxa)

configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readSamples()

Read reference ranges

configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readRefRanges()

Read haplotype ID matrix

configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readHaplotypeIds()

PHGDataSet objects

configFile |> 
    PHGLocalCon() |> 
    PHGMethod("PATH_METHOD") |> 
    readPHGDataSet()

maize-genetics/rPHG documentation built on April 4, 2024, 11:18 p.m.