getData: Retrieve Bgee RNA-seq or Affymetrix data.

In BgeeDB/BgeeDB_R: Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Retrieve Bgee RNA-seq or Affymetrix data.

Description

This function loads the quantitative expression data and presence calls for samples available from Bgee (rna_seq, affymetrix, sc_full_length).

Usage

getData(
  myBgeeObject,
  experimentId = NULL,
  sampleId = NULL,
  anatEntityId = NULL,
  stageId = NULL,
  cellTypeId = NULL,
  sex = NULL,
  strain = NULL,
  withDescendantAnatEntities = FALSE,
  withDescendantStages = FALSE,
  withDescendantCellTypes = FALSE
)

Arguments

myBgeeObject	A Reference Class Bgee object, notably specifying the targeted species and data type.
experimentId	Filter allowing to specify one or more ArrayExpress or GEO accession, e.g., GSE43721. Default is NULL: takes all available experiments for targeted species and data type.
sampleId	Filter allowing to specify one or more sample ID. Depending on the selected datatype this sample IDs can correspond to Chip IDs (affymetrix) or RNA-Seq library IDs (rna_seq). Default is NULL: takes all available samples for targeted species and data type.
anatEntityId	Filter allowing to specify one or more anatomical entity IDs from the UBERON ontology (http://uberon.github.io/). Default is NULL: takes all available anatomical entities for targeted species and data type.
stageId	Filter allowing to specify one or more developmental stage IDs from Developmental Stage Ontology (https://github.com/obophenotype/developmental-stage-ontologies). Default is NULL: takes all available developmental stages for targeted species and data type.
cellTypeId	Filter specific to single cell datatype (sc_full_length) allowing to specify one or more cell type IDs from the UBERON ontology (http://uberon.github.io/). Default is NULL: takes all available cell types for targeted species and data type. Available for Bgee 15.0 and after
sex	Filter allowing to specify one or more sexes. Default is NULL: takes all available sexes for targeted species and data type. Available for Bgee 15.0 and after
strain	Filter allowing to specify one or more strains. Default is NULL: takes all available strains for targeted species and data type. Available for Bgee 15.0 and after
withDescendantAnatEntities	Allows to filter on the selected anatEntityId and all its descendants. This functionality is available for Bgee 15.0 release and after
withDescendantStages	Allows to filter on the selected stageId and all its descendants. This functionality is available for Bgee 15.0 release and after
withDescendantCellTypes	Allows to filter on the selected cellTypeId and all its descendants. This functionality is available for Bgee 15.0 release and after

Value

Return a dataframe containing all Bgee processed expression data from the selected species and datatype using specified filters with operator AND.

Author(s)

Julien Wollbrett, Andrea Komljenovic and Julien Roux.

Examples

{
  bgee <- Bgee$new(species = "Mus_musculus", dataType = "rna_seq")
  dataMouseGSE43721 <- getData(bgee, experimentId = "GSE43721")
  dataMouseVariousFilters <- getData(bgee, experimentId = c("GSE43721", "GSE36026"), 
                             anatEntityId = c("UBERON:0002107", "UBERON:0000956", "UBERON:0002048"))
}

BgeeDB/BgeeDB_R documentation built on Jan. 14, 2024, 4:29 a.m.