calcGraphStats: A function to calculate the various summary statistics for...
In ScISI: In Silico Interactome

Description Usage Arguments Details Value Author(s)

This function takes a putative protein complex (given by comp) and a list of bait to prey associations, and from these two data-sets computes various summary statistics on the induced Y2H graph which include: edge proportion of sampled nodes (baits to prey); estimated population mean nodal degree; proportion of sampled baits with hits to baits with no hits; the average out degree of baits; the proteins (bait and prey) which are not isolated; the number of connected components to the y2h graph, etc.

1	calcGraphStats(comp, bait2PreyL)

comp

The comp argument is a character vector containing the constituent proteins of some putative protein complex

bait2PreyL

A named list of lists. Each name represents a particular Y2H experiment; within each experimental entry, there is two more lists: 1. bpList and 2. expList. bpList is a named list of character vectors; each name corresponds to a bait protein of that particular experiment, and the enry is a chracater vecotor of the hit proteins found as prey. the expList is a named list concerning experimental data: ActD gives the activation domain; GW is a logical denoting if the prey list is genome wide; and numBaits details the number of baits used in the experiment.

For the bait2PreyL; use the the intactInfo.rda data-set of the package y2hStat.

`complex`	A character vector of the constituent members of the proteinn complex of interest
`complexBait`	A character vector of those protein members which were also tested as baits in the y2h experiments
`b2CompP`	A character vector of all proteins which were tested as baits in the y2h experiments and also found a prey in the complex of interest
`notBait`	A character vector of those protein members which were not tested as baits
`avgDegOut`	The average out-degree of the bait proteins of the complex of interest
`notIsolated`	A character vector of proteins that showed experimental binary affiliation for some other complex member
`y2hGraph`	An instance of the class graph; a graphNEL induceds Y2H graph on the protein complex
`popMeanDegree`	The population mean degree derived from the bait proteins
`edgeProp`	The estimated edge proportions derived between undirected Y2H edges
`degBait`	A named list; each name corresponds to each member of the protein complex with the entry the number of proteins to which it is adjacent