pathway2RegulatoryGraph: This function generates the regulatory graph from the...

In rBiopaxParser: Parses BioPax files and represents them in R

Description

This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model.

This functions builds a graph from the pathway components of the supplied pathway. Only instances of class 'control' are considered, this leads a functinal graph with all edges either representing activations or inhibitions. No transports, no translocation, etc. If desired complexes can be split up into several nodes, this can sometimes lead to a more complex and cluttered graph. There can not be multiple edges between 2 nodes. Whenever duplicated edges are generated (especially by splitting up complexes) a warning is thrown.

Usage

pathway2RegulatoryGraph(
  biopax,
  pwid,
  expandSubpathways = TRUE,
  splitComplexMolecules = TRUE,
  useIDasNodenames = FALSE,
  verbose = TRUE
)

Arguments

biopax	A biopax model
pwid	string
expandSubpathways	logical. If TRUE subpathways are expanded into this graph, otherwise only this very pathway is used.
splitComplexMolecules	logical. If TRUE every complex is split up into its components. This leads to splitting a single node with name of the complex into several nodes with names of the components, these components all have identical edges.
useIDasNodenames	logical. If TRUE nodes of the graph are named by their molecule IDs instead of using the NAME property. This can help with badly annotated/formatted databases.
verbose	logical

Value

Returns the representing the regulatory graph of the supplied pathway in a node-edge-list graph.

Author(s)

Frank Kramer

Examples

 # load data
 data(biopaxexample)
 pwid1 = "pid_p_100002_wntpathway"
 pwid2 = "pid_p_100146_hespathway"
 mygraph = pathway2RegulatoryGraph(biopax, pwid1)
 plotRegulatoryGraph(mygraph)

Example output

Loading required package: data.table
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


Attaching package: 'graph'

The following object is masked from 'package:rBiopaxParser':

    combineNodes

Found 23 pathway components. Putting them together...
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P36 Controlleds:  P29
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P29 Controlleds:  P28 P26 P11
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P40 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P36 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P40 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P37 Controlleds:  P28 P11 P26
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P15 Controlleds:  P30
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P14 Controlleds:  P30
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P30 Controlleds:  P10 P25 P33 P12 P11 P13
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P32 Controlleds:  P10 P25 P33 P12
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P13 P11 P10 P25 P33 P12 Controlleds:  P27
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P10 P25 P33 P12 Controlleds:  P27
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P13 P11 P10 P25 P33 P12 Controlleds:  P17
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P10 P25 P33 P12 Controlleds:  P17
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P13 P11 P10 P25 P33 P12 Controlleds:  P18
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P10 P25 P33 P12 Controlleds:  P18
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P31 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P21 P20 P19 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P38 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P39 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - ACTIVATION Controllers:  P21 P20 P19 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P38 Controlleds:  P36
Adding to graph:  c("control", "control", "control") - INHIBITION Controllers:  P35 Controlleds:  P20 P19 P21
There were 19 warnings (use warnings() to see them)
Loading required package: Rgraphviz
Loading required package: grid

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.