get_active_pathway_ranking_metric: get_active_pathway_ranking_metric

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

Description

This function generates active pathway ranking metric for each cell/tissue type. It uses active pathway path and processed query data with a high expression threshold to generate the ranking metric.

Usage

get_active_pathway_ranking_metric(active.pathway.path, processed.query.data,
  high.exp.th)

Arguments

active.pathway.path	A list of active pathway path data for each cell/tissue type.
processed.query.data	A list with expressed query data where each sublist corresponds for each cell/tissue type.
high.exp.th	A high expression threshold value for the processed query data. It is used to get active (i.e., highly expressed) molecule proportion for each pathway path.

Details

This function generates active pathway ranking metric for each cell/tissue type. It uses active pathway path and processed query data with a high expression threshold to generate the ranking metric.

Value

This function returns a list of pathways' ranking metric for each cell/tissue type.

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)
## Get active pathway ranking metric
ROR1.active.pathway.ranking.metric<-get_active_pathway_ranking_metric(active.pathway.path = ROR1.active.pathway, processed.query.data = ROR1.processed.data, high.exp.th = 7)
head(sort(unlist(ROR1.active.pathway.ranking.metric$ROR1_LEC), decreasing=T))

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