extr_biodescr,BasicData-method {immcp}

Extract Biological descriptor

Description

Extract Biological descriptor

Usage

## S4 method for signature 'BasicData'
extr_biodescr(
  BasicData,
  geneset = c("kegg", "mkegg", "go", "wp"),
  arguments = list(minGSSize = 5, maxGSSize = 500, pvalue = 0.05, qvalue = 0.1),
  ref_type = "drug",
  ref = NULL,
  to_ENTREZID = TRUE
)

Arguments

BasicData

BasicData object.

geneset

Charactor vector, one of "kegg"(KEGG), "mkegg"(KEGG Module), "go"(GO-BP), and "wp"(WikiPathways); a data frame and list.

arguments

A list of the arguments of clusterProfiler, including minGSSize, maxGSSize, pvalue, and qvalue.

ref_type

Charactor vector, one of "drug", "herb", "compound" or "target", defaults to "drug".

ref

Charactor vector, reference drug, herb, compound or target, defaults to NULL.

to_ENTREZID

Logical, whether to translate to ENTREZID from SYMBOL, defaults to TRUE.

Value

A BioDescr object.

Examples

## Not run: 
data(drugdemo)
drug_herb <- PrepareData(drugdemo$drug_herb, from = "drug", to="herb")
herb_compound <- PrepareData(drugdemo$herb_compound, from = "herb", to="compound")
compound_target <- PrepareData(drugdemo$compound_target, from = "compound", to="target")
disease <- PrepareData(drugdemo$disease, diseaseID = "disease",from = "target", to="target")
BasicData <- CreateBasicData(drug_herb, herb_compound, compound_target, diseasenet = disease)
biodescr <- extr_biodescr(BasicData, geneset= "kegg")

## End(Not run)