extr_biodescr {immcp}

Extract Biological descriptor

Description

Extract Biological descriptor

Usage

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.

Author(s)

Yuanlong Hu