procope.examples
package of the src/
folder.NetworkReader
class.ProteinNetwork hart=null, pe=null; |
InputStream
to read network data from. In this case we create a GZIPInputStream
for on-the-fly decompression of GZIPed input files.NetworkComparison.weightsOverlap
function outputs pairs of numbers, each pair is a weight for the same
edge in both networks. Missing edges get an implicit weight of zero.List<Point> overlap = NetworkComparison.weightsOverlap(hart, pe, false); |
hart = hart.getCutOffNetwork(3); |
ComplexSet mips=null; |
System.out.println("Complex enrichment of Hart: " + |
ComplexSet mips_below50 = mips.copy(); |
ROC
class. The result is a list of ROCCurve
objects which we pass into the chart generation function of the ROCCurveHandler
class to create the plot and save it into a file. For the generation of the negative set, we use the original MIPS set.List<ROCCurve> curves = ROC.calculateROCCurves(networks, mips_below50, mips, null, false); |
CombinationRules rules = new CombinationRules(CombinationRules.CombinationType.INTERSECT); |
BooleanExpression
and pass this expression to the filter method of the ProteinNetwork
object. See also: Annotations and filteringBooleanExpression expression=null; |
ProteinNetwork
objects is iterable using the NetworkEdge
class. Note how the ProteinManager
is used to map back internal protein IDs to their String labels.for (NetworkEdge edge : filtered) { |
Loading networks...
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