getBrainStars: Get various information in BrainStars

In BrainStars: query gene expression data and plots from BrainStars (B*)

Description

This function queries various information from BrainStars The function is a wrapper of All BrainStars API.

Usage

  getBrainStars(query, type, base.url, json)

Arguments

query	keyword
type	BrainStars API name. (expression, search, probeset, marker, multistate, onestate, ntnh and genefamily)
base.url	URL of Brainstars database.
json	TRUE is json mode of response. (Defalut is FALSE)

Details

Brain API is for keyword search and is based on Tokyo Manifesto and TogoWS REST interface.

Type: expression (query) "query" is a vector of ProbeSet IDs.

Type: search, probeset and onestate Keyword for retrieving a list of hit entries: (query+string)[/(offset),(limit)].

Keyword for retrieving the count of hit entries: (query+string)/count.

Type: genefamily Keyword search format: (category)/(keyword)/(offset),(limit)

You can indicate gene category name in the following words:

• "tf": transcription factors

• "transmem": transmembrane genes

• "channel": channel genes

• "gpcr": GPCR genes

• "adhesion": cell adhesion genes

• "excellmat": extracellular matrix genes

• "structural": structural protein genes

• "neurogenesis": neurogenesis related genes

• "hox": homeobox genes

• "nucrcpt": nuclear receptor genes

• "ntnh": neurotransmitter/neurohormone genes

• "axon": axon guidance genes

• "fox": forkhead genes

Type: marker List API is for retrieving a list of gene marker candidates. Keyword search format: high,low/(region)/(offset),(limit).

Count of entriest search format: high,low/(region)/count.

"high" is highly expressed regions. "low" is low expressed regions. (region) means CNS region name.

Type: ntnh List API is for retrieving inferred connections among CNS regions by neurotransmitter/neurohormone (ntnh).

Keyword search format: high,low/(ligand-region)/(receptor-region)/(offset),(limit).

Count of entries search format: high,low/(ligand-region)/(receptor-region)/count.

"high": high state regions, "up": up state regions.

(ligand-region): Ligand CNS region. (receptor-region): Receptor CNS region.

Type: multistate List API is for retrieving a list of multi-state gene candidates. Keyword search format: high,up,low,down/(region)/(offset),(limit).

Count of entries search format: high,up,low,down/(region)/count.

"high": high state regions, "up": up state regions, "low": low state regions, "down": down state regions.

(region) means CNS region name.

output: If json is TRUE, you get response in JSON character. Dafault is matrix or list. If you chose "expression" type, you can get response in ExpressionSet. When you indicate "probeset" type, you can get annotations in list.

If the result has at least one hit entries, a matrix of entries is returned. If not, 404 Not found error code is returned. "offset,limit" can be used to retrieve a part of hit entries. If "offset,limit" is not given, all hits are returned.

If "count" was included in "query", the count of hit entries is returned in matrix, list, ExpressionSet or JSON format

Value

A matrix, ExpressionSet, list of annotation or character vector of Search API response in JSON.

Examples

my.search   <- getBrainStars(query = "receptor",   type = "search")
my.probeset <- getBrainStars(query = "1439627_at", type = "probeset")
my.tf       <- getBrainStars(query = "tf",         type = "genefamily")
my.eset     <- getBrainStars(query = "1439627_at", type = "expression")

my.probeset.json <- getBrainStars(
  query = "1439627_at",
  type = "probeset",
  json = TRUE
)

BrainStars documentation built on Nov. 8, 2020, 5:58 p.m.