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

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Installation

You can install R/GNapi from GitHub.

You first need to install the remotes package.

install.packages("remotes")

Then use remotes::install_github() to install R/GNapi.

library(remotes)
install_github("rqtl/GNapi")

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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)

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License

R/GNapi is released under the MIT license.