Reading and writing of coiled coil prediction model from/to files

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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

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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

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:

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    _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.

Value

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

Note

The PrOCoil model is available on on http://www.bioinf.jku.at/software/procoil/PrOCoilModel_v2.CCModel. in exactly the format the function readCCModel requires. Analogously for the alternative model optimized for balanced accuracy (see CCModel): http://www.bioinf.jku.at/software/procoil/PrOCoilModelBA_v2.CCModel. The original models described in [Mahrenholz et al., 2011] are available on http://www.bioinf.jku.at/software/procoil/PrOCoilModel_v1.CCModel and http://www.bioinf.jku.at/software/procoil/PrOCoilModelBA_v1.CCModel, respectively. So, by loading one of these files, the original models can still be used.

Author(s)

Ulrich Bodenhofer bodenhofer@bioinf.jku.at

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

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## 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

## Not run: 
## 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]

## End(Not run)