R/GNapi User Guide

The R/GNapi package provides access to the GeneNetwork2 API; for details on the API, see its documentation The present vignette simply follows that documenation and shows the corresponding R facilities.

Fetch species list

To fetch the list of species available in the GeneNetwork database:

list_species()

You can also get the information for a single species:

list_species("mouse")

Fetch Groups/RISets

To get a list of groups (for example, RIL sets) across all species:

list_groups()

You can also get the list of groups for a single species:

list_groups("rat")

Fetch genotypes for Group/RIset

g <- get_geno("BXD")

Fetch datasets

List datasets for a particular group.

list_datasets("bxd")

List a particular dataset.

list_datasets("bxd", "HC_M2_0606_P")

Fetch sample data for dataset

phe <- get_pheno("HSNIH-PalmerPublish")

Information for mRNA assay/probeset

list_datasets(dataset="HC_M2_0606_P")

Or provide group/riset

list_datasets("bxd", "HC_M2_0606_P")

Fetch individual phenotype info

list_datasets("bxd", "10001")

Fetch trait information

This is mostly information about QTL location (LRS score and marker). You need to provide a group and a trait, such as a probeset on a microarray:

info_pheno("HC_M2_0606_P", "1436869_at")

Or a traditional phenotype:

info_pheno("BXD", "10002")

You can provide a vector of trait identifiers:

info_pheno("BXD", c("10002", "10010", "10100"))

Fetch sample data for a single trait

ph <- get_pheno("HC_M2_0606_P", "1436869_at")

For mRNA expression/probeset

info_pheno("HC_M2_0606_P", "1436869_at")

For classical phenotypes

info_pheno("BXD", "10001")

Analyses

Gemma

out <- run_gemma("BXDPublish", "10015", use_loco=TRUE)

R/qtl

out <- run_rqtl("BXDPublish", "10015", method="em", interval_mapping=TRUE)

Correlations

out <- run_correlation("HC_M2_0606_P", "BXDPublish", "1427571_at")