Estimate false positive and false negative error probabilities

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Description

Estimate false positive and false negative error probabilities for complex comembership edges using a protein complex interactome gold standard

Usage

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estimateCCMErrorRates(m,GS,filterSystematic=TRUE,	
         obsPropThresh=1,SystematicpThresh=.01)

Arguments

m

The bait to prey data adjacency matrix. Baits index the rows and prey index the columns.

GS

A gold standard protein complex interaction incidence matrix. Proteins index the rows and protein complexes index the columns.

filterSystematic

A logical. If TRUE, all baits with with highly uneven directed degree will be filtered out of the data.

obsPropThresh

A numeric between 0 and 1. The proportion of tested proteins found within a protein complex needed to keep that protein complex within the gold standard set.

SystematicpThresh

A numeric between 0 and 1. The p-value threshold by which systematic errors are filtered.

Details

The model is described in the manuscript Estimating node degree in bait-prey graphs. by D. Scholtens et al.

Value

A list:

globalpTP

A numeric between 0 and 1. Estimate of pTP.

globalpTPSE

A numeric. Estimate of standard error of globalpTP estimate.

globalpFP

A numeric between 0 and 1. Estimate of pFP.

pTP95CI

A vector of length 2. 95 percent confidence interval upper and lower bounds for globalpTP estimate.

pFP95CI

A vector of length 2. 95 percent confidence interval upper and lower bounds for globalpFP estimate.

nEligComplexes

A numeric. Number of complexes from GS that met obsPropThresh criteria.

nEligBaits

A numeric. Total number of eligible baits in GS set.

nEligEdges

A numeric. Total number of eligible edges in GS set.

nBaitsInComplexes

A vector. Number of baits in each eligible complex.

complexSizes

A vector. Size of each complex in GS set.

Author(s)

T. Chiang and D. Scholtens

References

Scholtens D, Chiang T, Huber W, Gentleman R. Estimating node degree in bait-prey graphs. Bioinformatics. To appear.

Examples

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data(Ho2002BPGraph)
data(ScISIC)
Ho2002mat = as(Ho2002BPGraph,"matrix")
estimateCCMErrorRates(Ho2002mat,ScISIC)$globalpTP

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