R/GNapi - R package to connect to the GeneNetwork API

R/GNapi is an R package for connecting to the GeneNetwork API.

Installation

install.packages("GNapi", repos="https://rqtl.r-universe.dev")

Alternatively, install it from GitHub with the remotes package:

#install.packages("remotes")
library(remotes)
install_github("rqtl/GNapi")

Usage

For an understanding of the GeneNetwork API, see its documentation, as well as Zachary Sloan's tutorial.

The R/GNapi package has a set of functions for connecting to the GeneNetwork API to grab different bits of information or data.

check_gn() - Check connection.
list_species() - List available species.
list_groups("drosophila") - List available groups of datasets
list_datasets("BXD") - List available datasets for a given group (here, "BXD").
list_datasets(dataset="CB_M_1004_P") - Get meta information about a data set.
info_pheno("BXD", "10038") - Get summary information for a phenotype
get_pheno("BXD", "10646") - Get phenotype values for a classical trait.
get_geno("BXD") - Get genotypes for a group.
run_gemma("BXDPublish", "10015") - Perform a genome scan with gemma
run_rqtl("BXDPublish", "10015") - Perform a genome scan with R/qtl
run_correlation("HC_M2_0606_P", "BXDPublish", "1427571_at") - Finds traits that are correlated with a given trait.

For further examples, see the online vignette, which is also available from within R:

vignette("GNapi")

Note that we enforce a delay between calls to the API, to slow repeated calls within a loop. The default is 1 sec; it can be controlled with the option GNapi_delay. For example, to make the delay 0.5 seconds, use:

options(GNapi_delay=0.5)

License

R/GNapi is released under the MIT license.