apEX: Example data set for apComplex package

In apComplex: Estimate protein complex membership using AP-MS protein data

Description

A matrix and corresponding graph of AP-MS purifications from a small hypothetical experiment.

Usage

data(apEX)
data(apEXG)

Details

apEX is a matrix of hypothetical AP-MS data. The 4 rows correspond to bait proteins and the 8 columns correspond to proteins found as hits in the hypothetical experiment and are named accordingly. The first 4 column names are the same as the 4 row names; bait proteins can also be found as hits by other baits, hence their inclusion as columns in apEX. An entry of "1" in the ith row and jth column of apEX indicates that bait protein i found protein j as a hit. All other entries are "0". There are a total of 9 "1" entries in the matrix, corresponding to 9 comemberships detected in the experiment.

apEXG is a graphNEL object in which 8 nodes represent proteins and 9 directed edges represent comemberships detected in the purification. Each directed edge originates at the bait and ends at the hit. Each edge in apEXG corresponds to an entry of "1" in the apEX matrix.

These data are used in the apComplex vignette.

Examples

data(apEX)
apEX

data(apEXG)
adj(apEXG,"P1")

apComplex documentation built on Nov. 8, 2020, 7:43 p.m.