dot-biomartLoad: Common call to biomaRt to avoid repetitive code

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

Common call to biomaRt to avoid repetitive code

Description

Common call to biomaRt to avoid repetitive code

Usage

.biomartLoad(attributes, filters, values, useCache, verbose)

Arguments

attributes	Attributes you want to retrieve. A possible list of attributes can be retrieved using the function biomaRt::listAttributes.
filters	Filters (one or more) that should be used in the query. A possible list of filters can be retrieved using the function biomaRt::listFilters.
values	Values of the filter, e.g. vector of affy IDs. If multiple filters are specified then the argument should be a list of vectors of which the position of each vector corresponds to the position of the filters in the filters argument
useCache	Boolean indicating if biomaRt cache should be used
verbose	When using biomaRt in webservice mode and setting verbose to TRUE, the XML query to the webservice will be printed.

Value

data.frame with attributes as columns and values translated to them

See Also

geneNames

ensemblGeneNames

protein2EnsemblGeneNames

biomaRt::getBM()

biomaRt::useEnsembl()

Examples

glmSparseNet:::.biomartLoad(
    attributes = c("external_gene_name", "ensembl_gene_id"),
    filters = "external_gene_name",
    values = c("MOB1A", "RFLNB", "SPIC", "TP53"),
    useCache = TRUE,
    verbose = FALSE
)

sysbiomed/glmSparseNet documentation built on Feb. 17, 2024, 1:38 p.m.