scater (version 1.0.4)

getBMFeatureAnnos: Get feature annotation information from Biomart

Description

Use the biomaRt package to add feature annotation information to an SCESet.

Usage

getBMFeatureAnnos(object, filters = "ensembl_transcript_id", attributes = c("ensembl_transcript_id", "ensembl_gene_id", "mgi_symbol", "chromosome_name", "transcript_biotype", "transcript_start", "transcript_end", "transcript_count"), feature_symbol = "mgi_symbol", feature_id = "ensembl_gene_id", biomart = "ENSEMBL_MART_ENSEMBL", dataset = "mmusculus_gene_ensembl", host = "www.ensembl.org")

Arguments

object

an SCESet object

filters

character vector defining the "filters" terms to pass to the biomaRt::getBM function.

attributes

character vector defining the biomaRt attributes to pass to the attributes argument of getBM.

feature_symbol

character string defining the biomaRt attribute to be used to define the symbol to be used for each feature (which appears as the feature_symbol in fData(object), subsequently). Default is "mgi_symbol", gene symbols for mouse. This should be changed if the organism is not Mus musculus!

feature_id

character string defining the biomaRt attribute to be used to define the ID to be used for each feature (which appears as the feature_id in fData(object), subsequently). Default is "ensembl_gene_id", Ensembl gene IDs for mouse. This should be changed if the organism is not Mus musculus!

biomart

character string defining the biomaRt to be used. Default is "ENSEMBL_MART_ENSEMBL".

dataset

character string defining the biomaRt dataset to use. Default is "mmusculus_gene_ensembl", which should be changed if the organism is not the mouse!

host

optional character string argument which can be used to select a particular "host" from biomaRt to use. Useful for accessing archived versions of biomaRt data. Default is "www.ensembl.org", in which case the current version of the biomaRt (now hosted by Ensembl) is used.

Value

an SCESet object

Details

See the documentation for the biomaRt package, specifically for the functions useMart and getBM, for information on what are permitted values for the filters, attributes, biomart, dataset and host arguments.

Examples

## Not run: 
# object <- getBMFeatureAnnos(object)
# ## End(Not run)