createBPList {y2hStat} | R Documentation

## A function to create the Bait to Prey association list.

### Description

This function takes the indexSetAll, baitsSystematic, and preysSystematic entries respectively from the output list of the R function collectIntactData, and it generates a three tier-ed list which ultimately records the bait to prey association from each yeast 2-hybrid experiment obtained from the IntAct repository.

### Usage

    createBPList(indexSet, baitsSystematic, preysSystematic)

### Arguments

`indexSet` | A list of named lists. The names correspond to each experiment while the entries to the lower level lists are character vectors with two elements: the first element is the id for the bait protein and the second an id for the prey. This is an entry of the output of the collectIntactData function called indexSetAll
`baitsSystematic` | A named list. The names correspond to the IntAct acension codes for any proteins used as baits, and the entries of the list are character vectors consisting of Systematic gene names with respect to the IntAct ID. This is also an entry from the output of the function collectIntactData.
`preysSystematic` | A named list. The names correspond to the IntAct acension codes for any proteins used as preys, and the entries of the list are character vectors consisting of Systematic gene names with respect to the IntAct ID. This is also an entry from the output of the function collectIntactData.

### Value

This function generates a three tiered list. The top tier is the main list. The second tier-ed set of lists should be named or referenced by experimentors. The third tier is a list of bait to prey associations. The names in the third tier of the list are those proteins sampled as baits, and the entries are character vectors of proteins detected as prey. This function will restrict those prey proteins to those which have also been sampled as baits. The resulting character vector contains only prey also sampled as baits or as a character(0)

### Author(s)

T Chiang

### Examples

    data(y2h)
    eg = y2h$indexSetAll[3]
    eg1 = y2h$baitsSystematic[3]
    eg2 = y2h$preysSystematic[3]
    createBPList(eg, eg1, eg2)

[Package y2hStat version 1.2.0 Index]