Package 'GNapi'

Check if GeneNetwork is live

Description

Check if GeneNetwork is live

Usage

check_gn(url = gnapi_url())

Arguments

url	URL for GeneNetwork

Value

Character string.

Examples

check_gn()

---

Get genotype data

Description

Get genotype data

Usage

get_geno(group, url = gnapi_url(), format = "geno")

Arguments

group	Name of group
url	The URL for the GeneNetwork API
format	The group's genotypes format

Value

A data frame

See Also

get_pheno(), list_groups()

Examples

g <- get_geno("QSM")

---

Get phenotype data

Description

Get phenotype data

Usage

get_pheno(dataset, trait = NULL, url = gnapi_url())

Arguments

dataset	Short abbreviation for a dataset, or name of a group
trait	Optional trait name
url	The URL for the GeneNetwork API

Value

A data frame, with samples as rows and either traits as columns or with the columns being detailed information for a single trait

See Also

get_geno()

Examples

ph1 <- get_pheno("BXDPublish")
ph2 <- get_pheno("BXD", "10002")
ph3 <- get_pheno("HC_M2_0606_P", "1436869_at")

---

The URL for the GeneNetwork API

Description

The current URL for the GeneNetwork API

Usage

gnapi_url()

Value

The URL, as character string

Examples

gnapi_url()

---

Get summary information about a phenotype

Description

Get summary information about a phenotype

Usage

info_pheno(group, trait, url = gnapi_url())

Arguments

group	Name of a group of datasets
trait	Trait identifier (can be a vector)
url	The URL for the GeneNetwork API

Value

A data frame

Examples

info_pheno("BXD", "10002")
info_pheno("HC_M2_0606_P", "1436869_at")

---

List available datasets for a group

Description

List available datasets for a group.

Usage

list_datasets(group = NULL, dataset = NULL, url = gnapi_url())

Arguments

group	Name of group, as single character string
dataset	Optional name of a specific dataset
url	URL for GeneNetwork API

Value

A data frame with dataset ID, name, and description

See Also

list_species(), list_groups()

Examples

list_datasets("BXD")
list_datasets("BXD", "HC_M2_0606_P")
list_datasets(dataset="HC_M2_0606_P")

g <- list_groups()
d <- list_datasets(g$Name[8])
list_datasets(dataset=d$Short_Abbreviation[1])

list_datasets("bxd", "10001")

---

Get list of groups

Description

Get list of available groups

Usage

list_groups(species = NULL, url = gnapi_url())

Arguments

species	Optional species name, for just the groups for that species.
url	URL for GeneNetwork API

Value

Data frame with columns FullName, Id, Name, and TaxonomyId.

See Also

list_species(), list_datasets()

Examples

list_groups()
list_groups("barley")

---

Get list of species

Description

Get list of available species

Usage

list_species(species = NULL, url = gnapi_url())

Arguments

species	Optional character string, to obtain a particular, single species
url	URL for GeneNetwork API

Value

Data frame with columns FullName, Id, Name, and TaxonomyId.

See Also

list_groups(), list_datasets()

Examples

list_species()

---

Calculate correlations

Description

Find correlated traits in GeneNetwork

Usage

run_correlation(
  dataset,
  group,
  trait,
  type = c("sample", "tissue"),
  method = c("pearson", "spearman"),
  n_results = 500,
  url = gnapi_url()
)

Arguments

dataset	Name of database for the trait (Short_Abbreviation)
group	Target database name to be correlated against
trait	ID for trait used for correlation
type	Sample or tissue correlation
method	Pearson or Spearman correlation
n_results	Number of results to return
url	The URL for the GeneNetwork API

Value

Data frame

Examples

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

---

Run gemma

Description

Perform a genome scan using gemma

Usage

run_gemma(dataset, trait, use_loco = FALSE, maf = 0.01, url = gnapi_url())

Arguments

dataset	ID for dataset being used (Short_Abbreviation)
trait	ID for trait being mapped
use_loco	Whether to use LOCO (leave one chromosome out)
maf	Filter on minor allele frequency
url	The URL for the GeneNetwork API

Value

A data frame

Examples

out <- run_gemma("HC_M2_0606_P", "1418701_at")

---

Run R/qtl

Description

Perform a genome scan using R/qtl

Usage

run_rqtl(
  dataset,
  trait,
  method = c("hk", "ehk", "em", "imp", "mr", "mr-imp", "mr-argmax"),
  model = c("normal", "binary", "2part", "np"),
  n_perm = 0,
  control_marker = NULL,
  interval_mapping = FALSE,
  url = gnapi_url()
)

Arguments

dataset	ID for dataset being used (Short_Abbreviation)
trait	ID for trait being mapped
method	Indicates whether to use the EM algorithm, imputation, Haley-Knott regression, the extended Haley-Knott method, or marker regression.
model	The phenotype model: the usual normal model, a model for binary traits, a two-part model, or non-parametric analysis
n_perm	Number of permutations
control_marker	Name of marker to use as a covariate
interval_mapping	Whether to use interval mapping
url	The URL for the GeneNetwork API

Value

A data frame

Examples

out <- run_rqtl("HC_M2_0606_P", "1418701_at")

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