SubtypeDrug (version 0.1.9)

getDrugSpw: SubtypeDrug internal function

Description

According to the parameters set by the user, the up-regulatory and down-regulatory subpathway data of drug is obtained.

Usage

getDrugSpw(
  drug_target_data,
  spw_matrix_rnames,
  drug.P.value.threshold,
  drug.min.sz,
  drug.max.sz
)

Value

a list.

Arguments

drug_target_data

A list. A list stores a collection of drug up- and down-regulated subpathways.

spw_matrix_rnames

A vector. A vector consisting of row names of subpathway activity profile.

drug.P.value.threshold

A value. According to the threshold of the significant P value set by parameter `drug.p.val.threshold`, the drug up-regulation and down-regulatory subpathways were screened.

drug.min.sz

A numeric. The drug regulated subpathways intersects with the subpathways in the subpathway activity profile. Then drugs with less than `drug.spw.min.sz` up- or down-regulated subpathways are removed.

drug.max.sz

A numeric. Similar to parameter `drug.spw.min.sz`, drugs with more than `drug.spw.max.sz` up- or down-regulated subpathways are removed.

Author

Xudong Han, Junwei Han, Chonghui Liu

Details

getDrugSpw

Examples

require(GSVA)
Geneexp<-get("Geneexp")
UserGS<-get("UserGS")
UserDS<-get("UserDS")
gsvaPar <- GSVA::ssgseaParam(Geneexp,UserGS,minSize=2)
spw_matrix<-gsva(gsvaPar)
x<-getDrugSpw(UserDS,row.names(spw_matrix),0.05,1,100)