Overview

This package allows users to easily call the GA4GH API from R.

The functions are typically split into get_* and search_*. The get_* functions retrive an object from the API with a specified ID and the search_* functions post JSON to the API and retrieve the results.

Usage

The ga4gh_client function should be used to create a client to interact with the API.

client <- ga4gh_client("http://localhost", 9001)

This can then be used in the get and search functions. The %>% function from magrittr can simulate to some degree the client having methods, each method being one of the get or search functions. At the moment these functions return response objects from the httr package. Use content() to extract the content of the response as a list.

client %>% get_dataset("id") %>% content()

## find all the datasets in the Server
d <- client %>% search_datasets() %>% content()

## find all the variant sets in a dataset
var_sets <- client %>% search_variant_sets(d$datasets[[1]]$id) %>% content

## find the first 100 variants from a variant set in chromosome 1
variants <- client %>% search_variants(var_sets$variantSets[[1]]$id, reference_name = "1", page_size = 100) %>% content

Further work could include a way to parse these into a data.frame or similar R object that is easier to work with. For example:

vars_to_df <- function(vars) {
  
  l <- lapply(vars, function(x) c(unlist(x["referenceName"])[[1]], unlist(x["names"])[[1]], unlist(x["start"])[[1]], unlist(x["end"])[[1]],
                                  unlist(x["referenceBases"])[[1]], unlist(x["alternateBases"])[[1]]))
  
  df <- do.call(rbind, l) %>% data.frame(stringsAsFactors = FALSE)
  names(df) <- c("reference_name", "id", "start", "end", "reference_bases", "alternate_bases")
  df$start <- as.numeric(df$start)
  df$end <- as.numeric(df$end)
  df
}

This will turn the content of a search_variants response into a data.frame containing some of the fields. Ideally this should be more general. Work could be done to formalise each of the response objects returned from the various get and search functions. These are detailed in the interactive documentation on the GA4GH reference server http://1kgenomes.ga4gh.org/static/index.html