library(knitr) opts_chunk$set(fig.width=7, fig.height=4.5, dev.args=list(pointsize=16), eval=FALSE)
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.
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")
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")
g <- get_geno("BXD")
List datasets for a particular group.
list_datasets("bxd")
List a particular dataset.
list_datasets("bxd", "HC_M2_0606_P")
phe <- get_pheno("HSNIH-PalmerPublish")
list_datasets(dataset="HC_M2_0606_P")
Or provide group/riset
list_datasets("bxd", "HC_M2_0606_P")
list_datasets("bxd", "10001")
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"))
ph <- get_pheno("HC_M2_0606_P", "1436869_at")
info_pheno("HC_M2_0606_P", "1436869_at")
info_pheno("BXD", "10001")
out <- run_gemma("BXDPublish", "10015", use_loco=TRUE)
out <- run_rqtl("BXDPublish", "10015", method="em", interval_mapping=TRUE)
out <- run_correlation("HC_M2_0606_P", "BXDPublish", "1427571_at")
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