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Randomly sample a set of nodes from the gene pool, and check the number of edges contained, if there are edges among the nodes, return the random sub-network
● Data Source:
CranContrib
● Keywords:
● Alias: random_network_sampling_PPI
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GA_search_PPI
(Package: COSINE) :
Run genetic algorithm to search for the PPI sub-network
This function performs the stochastic search using genetic algorithm to find the globally optimal subnetwork which gives rise to the highest score defined by a scoring function, which measures the extent of the differential expression of the PPI subnetwork across several datasets.
● Data Source:
CranContrib
● Keywords:
● Alias: GA_search_PPI
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get_quantiles
(Package: COSINE) :
Get the five quantiles of the weight parameter lambda
Use random sampling to get a large number of subnetworks and then calculate the distribution of the ratio between the edge-score term and node-score term
● Data Source:
CranContrib
● Keywords:
● Alias: get_quantiles
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0 images
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This function performs the stochastic search using genetic algorithm to find the globally optimal subnetwork which gives rise to the highest score defined by a scoring function, which measures the extent of the differential expression of the subnetwork across several datasets.
● Data Source:
CranContrib
● Keywords:
● Alias: GA_search
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diff_gen
(Package: COSINE) :
Calculate the F-statistics and ECF-statistics
The "diff_gen" function calculates the F-statistics which measures the differential expression of each gene and the ECF-statistcs which measures the differential correlation of each gene pair between two datasets
● Data Source:
CranContrib
● Keywords:
● Alias: diff_gen
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f.test
(Package: COSINE) :
To get the F-statistics for each gene
Calculate the F-statistics measuring the differential expression of each gene
● Data Source:
CranContrib
● Keywords:
● Alias: f.test
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get_components_PPI
(Package: COSINE) :
Get all the components (connected clusters) of the sub-network
Map the edges in the selected sub-network to the background PPI network and get all the clusters with size larger than the minimumset by the user
● Data Source:
CranContrib
● Keywords:
● Alias: get_components_PPI
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diff_gen_for3
(Package: COSINE) :
Generate the F-statistics and ECF-statistics for the
It works very similarly to "diff_gen" except that it performs the calculation across three rather than two datasets
● Data Source:
CranContrib
● Keywords:
● Alias: diff_gen_for3
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score_scaling
(Package: COSINE) :
To get the normalzied F-statistics and ECF-statistics
Perform standardization of the node score and edge score
● Data Source:
CranContrib
● Keywords:
● Alias: score_scaling
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diff_gen_PPI
(Package: COSINE) :
Generate the scaled node score and scaled
Compute the F-statistic and ECF-statistic and then standardize them
● Data Source:
CranContrib
● Keywords:
● Alias: diff_gen_PPI
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0 images
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