diceCoefficient: diceCoefficient

In Babulab-bioc/MSiP: 'MassSpectrometry' Interaction Prediction

Description

This function applies Dice coefficient to score instances (e.g., bait-prey interactions (BPIs) in the data.frame.The Dice coefficient was first applied by Zhang et al., 2008 to score interactions between all identified proteins (baits and preys) in a given AP-MS experiment.

Usage

diceCoefficient(datInput)

Arguments

datInput

Data frame with column names: Experiment.id, Replicate, Bait, Prey, and count (i.e., prey count).

Value

Data frame containing bait-prey pairs with Dice coefficient score, a number between 0 and 1

Author(s)

Matineh Rahmatbakhsh, [e-mail]

References

Zhang, B., Park, B.-H., Karpinets, T., and Samatova, N. F. (2008). From pull-down data to protein interaction networks and complexes with biological relevance. Bioinformatics 24, 979-986.

Examples

data(SampleDatInput)
datScoring <- diceCoefficient(SampleDatInput)
head(datScoring)

Babulab-bioc/MSiP documentation built on Dec. 17, 2021, 9:52 a.m.