Check a pair of pathways are captured in the signature model

Source: R/checkPathwaySeparation.R

Arguments pathway1 and pathway2 are character vectors containing lists of pathways that you want to separate through the model.

checkPathwaySeparation(
  RAVmodel,
  pathway1,
  pathway2,
  cutoff_nes = NULL,
  cutoff_n = 5
)

Arguments

RAVmodel

PCAGenomicSignatures object.

pathway1

A character vector. Keywords you are looking for.

pathway2

A character vector. Keywords you are looking for.

cutoff_nes

A minimum NES to be kept. Under the default (NULL), this filter is not used.

cutoff_n

A number of pathways to keep.Default is 5. If you don't want to use this filter, assign it as NULL.

Note

https://github.com/greenelab/multi-plier/blob/master/32-explore_pathway_separation.Rmd