generate_pathway_path: generate_pathway_path

In VCCRI/SPAGI: SPAGI: Identification of active signalling pathways by integrating gene expression and protein interaction network

Description

This function generates the background pathway path data using the list object returned by the function combine_mm_hs_ppi.

Usage

generate_pathway_path(ppi.result, housekeeping.gene, max.path.length = 7)

Arguments

ppi.result	The list object returned by the function combine_mm_hs_ppi.
housekeeping.gene	A vector consisting of housekeeping genes. This data is loaded automatically with the package. This data was generated using the gene expression profiles of different cell types and/or tissues from the ENCODE human and mouse project.
max.path.length	An integer number indicating the maximum path length. Default is 7.

Details

This function generates the background pathway path data using the list object returned by the function combine_mm_hs_ppi.

Value

This function returns a list consisting of the pathway path data that will be used as background data for the SPAGI package.

Examples

## Need two folder at working directory for downloading stringdb files for each species - stringdb_mouse, stringdb_human.
## It takes some time to download the data, and then can reuse the downloaded data.
## Here we will use RP.protein, KN.protein, TF.protein protein parameters. These data are automatically loaded with the package. You can modify these parameters.
## We will generate PPI data for two species - "mmusculus" and "hsapiens" by calling the function get_ppi_for_molecules two times.
## Then we will combine these two PPI data sets by using the combine_mm_hs_ppi function that will be used to generate the pathway path data.
## Finally we will generate the pathway path data using the combined PPI data

## Get PPI data for the protein molecules of species "mmusculus".
mm.ppi<-get_ppi_for_molecules(RP.protein, KN.protein, TF.protein, species="mmusculus")
## Get PPI data for the protein molecules of species "hsapiens".
hs.ppi<-get_ppi_for_molecules(RP.protein, KN.protein, TF.protein, species="hsapiens")
## Now combine and get the filtered PPI and the RP and TF proteins of the combined filtered PPI
comb.ppi.result<-combine_mm_hs_ppi(mm.ppi, hs.ppi, RP.protein, KN.protein, TF.protein)
##Generate the pathway path data using the comb.ppi.result and housekeeping.gene data sets
pathway.path<-generate_pathway_path(ppi.result=comb.ppi.result, housekeeping.gene)
head(summary(pathway.path))

VCCRI/SPAGI documentation built on May 23, 2019, 1:08 p.m.