identify_active_pathway_path: identify_active_pathway_path

In humayun2017/SPAGI: SPAGI: Signalling Pathway Analysis for putative Gene regulatory network Identification

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(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

## Here we will use "pathway.path" as background data from the SPAGI repository.
## Also we will use "ROR1.data" as query RNA-seq gene expression data. This data is for ocular lens epithelial cell differentiated from human pluripotent stem cells.
## These data sets are loaded automatically with the package.

## Pre-process the query data (ROR1.data), the data has already been made in CPM and log2 normalized format.
ROR1.processed.data<-preprocess_querydata(cell.tissue.data = ROR1.data, exp.cutoff.th = 1.8)
## Identify active pathway paths of the processed query data
ROR1.active.pathway<-identify_active_pathway_path(pathway.path = pathway.path, processed.query.data = ROR1.processed.data)
head(ROR1.active.pathway$ROR1_LEC$FGFR1)

humayun2017/SPAGI documentation built on May 13, 2019, 1:35 p.m.