identify_active_pathway_path_new: identify_active_pathway_path_new

In humayun2017/SPAGI2: SPAGI2: Identification of active signalling pathways for cross-species by integrating gene expression and human protein interaction network

Description

This function identifies active pathway paths for RNA-seq gene expression profile. It utilizes background pathway path data to identify the active pathway paths.

Usage

identify_active_pathway_path_new(pathway.path, processed.query.data)

Arguments

pathway.path	A list with pathway path data where each sublist denotes a path of the pathway. This is used as background data.
processed.query.data	A list with expressed query data where each sublist corresponds for each cell/tissue type.

Details

This function identifies active pathway paths for RNA-seq gene expression profile. It utilizes background pathway path data to identify the active pathway paths.

Value

This function returns a list of pathways where each sublist denote a path of the pathway.

Examples

#Pre-process the 'tooth.epi.E13.5' data
tooth.epi.E13.5.processed.data<-preprocess_querydata_new(cell.tissue.data = tooth.epi.E13.5, exp.cutoff.th = 5.0, species="mmusculus")
#Generate the homology data for the two species - 'hsapiens' and 'mmusculus'
mouse.homology.data<-generate_homology_data(species1 = "hsapiens", species2 = "mmusculus")
#Generate the mouse homology pathway path data
mouse.homology.pathway.path<-generate_homology_pathways(species.homology.data = mouse.homology.data, pathway.path = pathway.path.new)
#Identify active pathway paths of the processed query data
tooth.epi.E13.5.active.pathway<-identify_active_pathway_path_new(pathway.path = mouse.homology.pathway.path, processed.query.data = tooth.epi.E13.5.processed.data)
head(summary(tooth.epi.E13.5.active.pathway$E13.5_Epi))

humayun2017/SPAGI2 documentation built on Aug. 5, 2020, 12:06 a.m.