BgeeDB (version 1.0.2)

Bgee-class: Retrieving the Bgee database data

Description

A Reference Class to give annotation available on Bgee for particular species and the requested data (rna_seq, affymetrix)

Value

• A get_annotation() list, lists the annotation of experiments for chosen species.
• A get_data(), if empty returns a list of experiments, if chosen experiment ID, then returns the dataframe of the chosen experiment; for chosen species
• A format_data(), transforms the data into matrix of expression values, e.g. RPKMs or raw counts

Fields

species

A character of species name as listed from Bgee. The species are:

• "Anolis_carolinensis"
• "Bos_taurus"
• "Caenorhabditis_elegans"
• "Danio_rerio"
• "Drosophila_melanogaster"
• "Gallus_gallus"
• "Gorilla_gorilla"
• "Homo_sapiens"
• "Macaca_mulatta"
• "Monodelphis_domestica"
• "Mus_musculus"
• "Ornithorhynchus_anatinus"
• "Pan_paniscus"
• "Pan_troglodytes"
• "Rattus_norvegicus"
• "Sus_scrofa"
• "Xenopus_tropicalis"

Homo sapiens is default species.

datatype

A character of data platform. Two types of datasets can be downloaded:

• "rna_seq"
• "affymetrix"

By default, RNA-seq data is retrieved from database.

experiment.id

A character. On default is NULL: takes all available data for that species. If GSE[0-9]+: takes specified experiment, eg. GSE30617.

data

A dataframe of downloaded Bgee data.

calltype

A character. There exist two types of expression calls in Bgee - present and absent.

• "expressed"
• "all"

User can retrieve only expressed (present) calls, or mixed (present and absent) calls. The default is expressed (present) calltype.

stats

A character. The expression values can be retrieved in RPKMs and raw counts:

• "rpkm"
• "counts"

The default is RPKMs.

Details

The expression calls come from Bgee (http://r.bgee.org), that integrates different expression data types (RNA-seq, Affymetrix microarray, ESTs, or in-situ hybridizations) in multiple animal species. Expression patterns are based exclusively on curated "normal", healthy, expression data (e.g., no gene knock-out, no treatment, no disease), to provide a reference of normal gene expression. This Class retrieves annotation of all experiments in Bgee database (get_annotation), downloading the data (get_data), and formating the data into expression matrix (format_data). See examples and vignette.

Examples

{
 bgee <- Bgee$new(species = "Mus_musculus", datatype = "rna_seq")
 annotation_bgee_mouse <- bgee$get_annotation()
 data_bgee_mouse <- bgee$get_data()
 data_bgee_mouse_gse30617 <- bgee$get_data(experiment.id = "GSE30617")
 gene.expression.mouse.rpkm <- bgee$format_data(data_bgee_mouse_gse30617,
 calltype = "expressed", stats = "rpkm")
 }