procoil (version 2.0.2)

CCModel-FileOps: Reading and writing of coiled coil prediction model from/to files

Description

Functions for reading a coiled coil prediction models from a file into a CCModel object and writing a CCModel object to a file.

Usage

readCCModel(file)
   writeCCModel(object, file)

Arguments

file

the name of the file from which readCCModel should read the model / the name of the file to which writeCCModel should write the model

object

the CCModel object that writeCCModel should write to a file

Value

• Upon successful completion, readCCModel returns a CCModel object. writeCCModel returns an invisible NULL.

Details

The procoil package comes with two ready-made models for oligomerization prediction, PrOCoilModel and PrOCoilModelBA. In case the user wants to define custom models or wishes to use previous versions of the prediction models, the functions readCCModel and writeCCModel can be used to read/write models from/to plain text files that can be viewed and also modified. writeCCModel writes models in the following format: _b,-1.07262284445085 _m,5 _scaling,1 L...Vd...a,1.63626232200227 R....Eg....e,1.5382098040217 R.Ec.e,1.29025032360792 E..Ve..a,1.22837780239385 ... Correspondingly, readCModel expects the file to conform to the above format. See CCModel for an overview of model parameters and an explanation of patterns and weights.

References

http://www.bioinf.jku.at/software/procoil/

Mahrenholz, C.C., Abfalter, I.G., Bodenhofer, U., Volkmer, R., and Hochreiter, S. (2011) Complex networks govern coiled coil oligomerization - predicting and profiling by means of a machine learning approach. Mol. Cell. Proteomics 10(5):M110.004994. DOI: 10.1074/mcp.M110.004994

See Also

procoil, CCModel-class

Examples

## load small example model file for testing purposes
## NOTE: this is an incomplete model that will probably not provide
##       meaningful predictions
file <- system.file("examples", "testModel.CCModel", package="procoil")
testModel <- readCCModel(file)

testModel

## read original model from file
URL <- "http://www.bioinf.jku.at/software/procoil/PrOCoilModel_v1.CCModel"
PrOCoilModelV1 <- readCCModel(URL)

## display summary of example model
PrOCoilModelV1

## display 10 heightes pattern weights
weights(PrOCoilModelV1)[1:10]