PRS_wrapper {ToPASeq} | R Documentation |
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.
PRS_wrapper(x, group, pathways, type, which = "proteins", edgeType = NULL, 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)
x |
An |
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 |
type |
Type of the input data, |
which |
Character, which type of nodes is preserved in a pathway. Possible values are |
edgeType |
Character, which type of edges is preserved in a pathway. If |
preparePaths |
Logical, by default the pathways are transformed with |
norm.method |
Character, the method to normalize RNAseq data. If |
test.method |
Character, the method for differentiall expression analysis of RNAseq data. If |
p.th |
Numeric, threshold for p-values of tests for differential expression of genes. Use |
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 |
A list:
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 |
Ivana Ihnatova
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
if (require(breastCancerVDX)) { data("vdx") pathways<-pathways("hsapiens","biocarta")[1:3] MAdata<-Biobase::exprs(vdx)[,1:10] rownames(MAdata)<-Biobase::fData(vdx)[,"Gene.symbol"] MAdata<-MAdata[!duplicated(rownames(MAdata)),] PRS_wrapper(MAdata, Biobase::pData(vdx)[,"er"][1:10], pathways, type="MA", convertTo="SYMBOL", logFC.th=-1, nperm=100) }