get_expression: Get expression data for given genes and brain structure IDs

In sgrote/ABAEnrichment: Gene expression enrichment in human brain regions

Description

Expression data obtained from the Allen Brain Atlas project [1-4].

Usage

    get_expression(structure_ids, gene_ids, dataset = "adult")

Arguments

structure_ids	vector of brain structure IDs, e.g. 'Allen:10208'.
gene_ids	vector of gene identifiers, either Entrez-ID, Ensembl-ID or gene-symbol.
dataset	'adult' (default) for the microarray dataset of adult human brains; '5_stages' for RNA-seq expression data of the developing human brain, grouped into 5 developmental stages; 'dev_effect' for a developmental effect score.

Details

Get gene expression in defined brain regions from adult or developing humans, or a developmental effect score for the developing human brain. Expression data is obtained from the Allen Brain Atlas project [1-4], averaged across donors, and for the developing human brain divided into five major age categories. The developmental effect score is based on expression data of the developing human brain. If a requested brain region has no expression data annotated, data from sampled substructures of this region is returned.
Please refer to the ABAData package vignette for details on the datasets.

Value

A matrix with expression values or developmental effect scores per brain region (rows) and gene (columns).
For expression data from the developing human brain ('5_stages') it is a list with an expression matrix for each of the 5 developmental stages.

Author(s)

Steffi Grote

References

[1] Hawrylycz, M.J. et al. (2012) An anatomically comprehensive atlas of the adult human brain transcriptome, Nature 489: 391-399. doi: 10.1038/nature11405
[2] Miller, J.A. et al. (2014) Transcriptional landscape of the prenatal human brain, Nature 508: 199-206. doi: 10.1038/nature13185
[3] Allen Institute for Brain Science. Allen Human Brain Atlas. Available from: http://human.brain-map.org/
[4] Allen Institute for Brain Science. BrainSpan Atlas of the Developing Human Brain. Available from: http://brainspan.org/

See Also

browseVignettes("ABAEnrichment")
browseVignettes("ABAData")
plot_expression
aba_enrich
get_name
get_id
get_sampled_substructures
get_annotated_genes

Examples

 
## get expression data of six genes in two brain regions 
## from the developing human brain, 
## each of the five list elements corresponds to an age category 
get_expression(structure_ids=c('Allen:10657','Allen:10208'),
    gene_ids=c('ENSG00000168036','ENSG00000157764','ENSG00000182158',
    'ENSG00000147889'), dataset='5_stages')

## see the package vignette for more examples

sgrote/ABAEnrichment documentation built on July 15, 2019, 9:38 p.m.