README.md

In c5sire/brapix: Additional Convenience Tools to Tnteract with BrAPI Compatible Databases

brapix

The goal of brapix is to provide eXtra tools for convenient bulk download breeding data and also do quick summaries and quality checks.

Installation

You can install brapix from github with:

# install.packages("devtools")

devtools::install_github("c5sire/brapix")

Example

This is a basic example which shows you how to solve a common problem:

library(brapi)
#> This is the development version of the 'brapi' package!
#> You are using version  0.9.9036 
#> 
#>  Please register any issues at: https://github.com/CIP-RIU/brapi/issues
library(brapix)
library(magrittr)


con <- ba_db()$germinate_test

loc <- ba_locations(con, pageSize = 10000)
#> URL call was: https://ics.hutton.ac.uk/germinate-demo/cactuar/brapi/v1/locations?page=0&pageSize=10000
#> Server status:  ok!
#> Returning page 0 (max. 0) with max. 10000 items (out of a total of 508).

ba_describe(loc)
#> n locations = 508
#> n locations with missing lat/lon = 0 (0%)

gmp <- ba_genomemaps(con = con)
#> URL call was: https://ics.hutton.ac.uk/germinate-demo/cactuar/brapi/v1/maps/?page=0&pageSize=30&species=&type=&
#> Server status:  ok!
#> Returning page 0 (max. 0) with max. 30 items (out of a total of 1).

gmp
#> # A tibble: 1 x 4
#>   mapDbId name        markerCount linkageGroupCount
#> * <chr>   <chr>             <int>             <int>
#> 1 1       All markers        4985                 7

ba_genomemaps_details(con, mapDbId = "1") %>% ba_chart()
#> URL call was: https://ics.hutton.ac.uk/germinate-demo/cactuar/brapi/v1/maps/1/
#> Server status:  ok!
#> Returning page 0 (max. 0) with max. 1 items (out of a total of 1).

c5sire/brapix documentation built on May 28, 2019, 4:35 p.m.