parseNCInetwork: Takes a NCI network and transforms it into a simpler graph...
In NCIgraph: Pathways from the NCI Pathways Database

Description Usage Arguments Value Author(s) Examples

Takes a NCI network and transforms it into a simpler graph only representing inhibition/activation relationships between genes.

1	parseNCInetwork(g, propagateReg=TRUE, separateEntrez=TRUE, mergeEntrezCopies=TRUE, entrezOnly=TRUE)

`g`	A `graph` object.
`propagateReg`	A `logical`. If `TRUE`, use propagateRegulation to transform the network before parsing it.
`separateEntrez`	A `logical`. If `TRUE`, don't merge two nodes with entrezID.
`mergeEntrezCopies`	A `logical`. If `TRUE`, merge resulting nodes that have the same entrezID.
`entrezOnly`	A `logical`. If `TRUE`, only keep nodes with an entrezID property.

The new graph object.

Laurent Jacob

## Load NCIgraph

library(NCIgraph)

## Get some raw networks

data("NCIgraphVignette", package="NCIgraph")

## Parse the first of them

parsedNetwork <- parseNCInetwork(NCI.demo.cyList[[1]],propagateReg=TRUE,separateEntrez=TRUE,mergeEntrezCopies=TRUE,entrezOnly=TRUE)

Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min