convertIdentifiersByVector: Convert pathway identifiers
In ToPASeq: Topology-based pathway analysis of RNA-seq data

Description Usage Arguments Value Author(s) See Also Examples

This function converts identifiers of nodes in a pathway. It uses the user specified named vector for the conversion.

1	convertIdentifiersByVector(pathway, conv.table)

`pathway`	An object of class `Pathway`
`conv.table`	A data.frame, in which the first column contains the type and the identifiers present in the pathway separeated by `:` and the second column contains the new identifiers and the third columns contains the types of the new identifiers

A Pathway with new identifiers of the nodes

Ivana Ihnatova

Pathway-class

g<-pathways("hsapiens","kegg")
ng<-sapply(g, function(x) length(nodes(x,"mixed")))
g<-g[[which.min(ng)]]
conv<-data.frame(orig=nodes(g,"mixed"), new=LETTERS[seq_len(min(ng))],newtype=rep("LETTERS",min(ng)))
gc<-convertIdentifiersByVector(g, conv.table = conv)@protEdges