deepblue_count_gene_ontology_terms: count_gene_ontology_terms

In MPIIComputationalEpigenetics/DeepBlueR: DeepBlueR

Description

Summarize the controlled_vocabulary fields, from experiments that match the selection criteria. It is similar to the 'collection_experiments_count' command, but this command return the summarization for all controlled_vocabulary terms.

Usage

deepblue_count_gene_ontology_terms(genes = NULL, go_terms = NULL,
  chromosome = NULL, start = NULL, end = NULL, gene_model = NULL,
  user_key = deepblue_options("user_key"))

Arguments

genes	- A string or a vector of string (Name(s) or ENSEMBL ID (ENSGXXXXXXXXXXX.X ) of the gene(s).)
go_terms	- A string or a vector of string (gene ontology terms - ID or label)
chromosome	- A string or a vector of string (chromosome name(s))
start	- A int (minimum start region)
end	- A int (maximum end region)
gene_model	- A string (the gene model)
user_key	- A string (users token key)

Value

faceting - A struct (Map with the mandatory fields of the experiments metadata, where each contains a list of terms that appears.)

See Also

Other Gene models and genes identifiers: deepblue_list_gene_models, deepblue_list_genes, deepblue_select_genes

Examples

gene_names = c('CCR1', 'CD164', 'CD1D', 'CD2', 'CD34', 'CD3G', 'CD44')
deepblue_count_gene_ontology_terms (genes = gene_names, gene_model = "gencode v23")

MPIIComputationalEpigenetics/DeepBlueR documentation built on Aug. 11, 2021, 4:12 p.m.