CCModel-FileOps {procoil} | R Documentation

## 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

### 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.

### 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

    ## 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)

[Package procoil version 2.12.0 Index]