listAttributes: lists the attributes available in the selected dataset

In grimbough/biomaRt: Interface to BioMart databases (i.e. Ensembl)

lists the attributes available in the selected dataset

Description

Attributes are the outputs of a biomaRt query, they are the information we want to retrieve. For example if we want to retrieve all EntrezGene identifiers of genes located on chromosome X, entrezgene_id will be the attribute we use in the query. The listAttributes function lists the available attributes in the selected dataset.

Usage

    listAttributes(mart, page,what = c("name","description","page"))
    searchAttributes(mart, pattern)

Arguments

mart	object of class Mart created using the useMart function
page	Show only the attributes that belong to the specified attribute page.
what	vector of types of information about the attributes that need to be displayed. Can have values like name, description, fullDescription, page
pattern	Character vector defining the regular expression (regex) to be used for the search. If left blank the default is to use ".*" which will match everything.

Author(s)

Steffen Durinck, Mike Smith

Examples

if(interactive()){

    ## list the available Ensembl marts and use Ensembl Genes
    listEnsembl()
    ensembl <- useEnsembl(biomart = "ensembl", dataset = 'hsapiens_gene_ensembl')

    ## list the available datasets in this Mart
    listAttributes(mart = ensembl)

    ## the list of attributes is very long and gets truncated by R
    ## we can search for a term of interest to filter this e.g. 'start'
    searchAttributes(mart = ensembl, pattern = "start")
    
    ## filter the attributes to give only entries containing 'entrez' or 'hgnc'
    searchAttributes(mart = ensembl, 'entrez|hgnc') 
}

grimbough/biomaRt documentation built on Feb. 11, 2024, 8:20 p.m.