Model parameters for the LOGICOIL prediction algorithm.

Description

A list containing five elements, each of which are required to run the LOGICOIL prediction algorithm.

Usage

data(Model_Parameters)

Format

A list containing five elements, which are required to run the LOGICOIL model:

1. amino: a character vector containing allowed amino-acids.

2. register: a character vector containing allowed register assignments.

3. amino_interactions: a 87 x 2 matrix containing all amino-amino interactions considered in the LOGICOIL model.

4. register_interactions: a 87 x 2 matrix containing the matching register positions of the amino-amino interactions.

5. lag_matrix: a 7 x 7 matrix that gives the positional lag between register positions.

Source

DOI: 10.1093/bioinformatics/bts648

References

Thomas L. Vincent, Peter J. Green and Dek N. Woolfson. "LOGICOIL-multi-state prediction of coiled-coil oligomeric state", 29(1), pp69-76, Bioinformatics, (2013). DOI: 10.1093/bioinformatics/bts648

Examples

data(Model_Parameters)
names(Model_Parameters)

# Optional to run
# summary(Model_Parameters$amino)
# summary(Model_Parameters$register)
# head(Model_Parameters$amino_interactions, 5)
# head(Model_Parameters$register_interactions, 5)
# Model_Parameters$lag_matrix

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(LOGICOIL)
Loading required package: nnet
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/LOGICOIL/Model_Parameters.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Model_Parameters
> ### Title: Model parameters for the LOGICOIL prediction algorithm.
> ### Aliases: Model_Parameters
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Model_Parameters)
> names(Model_Parameters)
[1] "amino"                 "register"              "amino_interactions"   
[4] "register_interactions" "lag_matrix"           
> 
> # Optional to run
> # summary(Model_Parameters$amino)
> # summary(Model_Parameters$register)
> # head(Model_Parameters$amino_interactions, 5)
> # head(Model_Parameters$register_interactions, 5)
> # Model_Parameters$lag_matrix
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>