deepblue_count_gene_ontology_terms: count_gene_ontology_terms

Description Usage Arguments Value See Also Examples

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

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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

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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 May 8, 2019, 3:19 p.m.