PRS: Function to use PRS method on microarray or RNA-Seq data

Description

A function runs PRS method on a gene expression data matrix or count matrix and vector dividing samples into two groups and a set of pathways from graphite package. The PRS method (please see Reference for the details) was adapted to graphite's graphs where each node is represented only by one gene.

Usage

PRS(x, group, pathways, type, preparePaths=TRUE, norm.method=NULL, test.method=NULL, p.th=0.05, logFC.th=2, nperm=1000, both.directions=TRUE, maxNodes=150, minEdges=0, commonTh=2, filterSPIA=FALSE, convertTo="none", convertBy=NULL)

Arguments

An ExpressionSet object or a gene expression data matrix or count matrix, rows refer to genes, columns to samples

group

Name or number of the phenoData column or a character vector or factor that contains required class assigments

pathways

A list of pathways in a form from graphite package or created by preparePathways()

type

Type of the data, "MA" for microarray, "RNASeq" for RNA-Seq, DEtable data.frame from differential expression analysis, or DEGlist a list of: log fold-changes of differentially expressed genes and names of the all genes analyses

preparePaths

Logical, by default the pathways are transformed with preparePathways(). Use FALSE, if you have done this transformation separately

norm.method

Character, the method to normalize RNAseq data. If NULL then TMM-normalization is performed. Possible values are: "TMM", "DESeq2", "rLog", "none". Ignored for type: "MA","DEtable", "DElist"

test.method

Character, the method for differentiall expression analysis of RNAseq data. If NULL then "voomlimma" is used. Possible values are: "DESeq2", "voomlimma", "vstlimma", "edgeR". Ignored for type: "MA","DEtable", "DElist"

p.th

Numeric, threshold for p-values of tests for differential expression of genes. Use 1 if you don't want any threshold to be applied

logFC.th

Numeric, threshold for log fold-change of a gene to identify the gene as differentially expressed. Use negative if you don't want any threshold to be applied

nperm

Numeric, number of permutations

both.directions, maxNodes, minEdges, commonTh, filterSPIA, convertTo, convertBy

Arguments for the preparePathways()

Value

res: A data frame with normalized score, p-value and FDR-adjusted p-value for each pathway
topo.sig: A list with log fold-changes and number of downstream differentially expressed nodes for nodes of individual pathways
degtest: A named vector of statistics from testing the differential expression of genes

References

Maysson Al-Haj Ibrahim, Sabah Jassim, Michael Anthony Cawthorne, and Kenneth Langlands. A Topology-Based Score for Pathway Enrichment, Journal of Computational Biology. May 2012, 19(5): 563-573

Examples

Run this code


if (require(DEGraph)) {
  data("Loi2008_DEGraphVignette")
  pathways<-pathways("hsapiens","biocarta")[1:10]
  PRS( exprLoi2008, classLoi2008, pathways, type="MA",  logFC.th=-1, nperm=100)
}
## Not run: 
# if (require(gageData)) {
# 
#  data(hnrnp.cnts)
#  hnrnp.cnts<-hnrnp.cnts[rowSums(hnrnp.cnts)>0,]
#  group<-c(rep("sample",4), rep("control",4))
#  pathways<-pathways("hsapiens","biocarta")[1:10]
#  PRS(hnrnp.cnts, group, pathways, type="RNASeq", logFC.th=-1, nperm=100, test="vstlimma")
# }
# ## End(Not run)