Description Usage Arguments Details Value Author(s) References Examples

View source: R/plot_LOGICOIL.R

This function can be used to plot the results of applying the LOGICOIL prediction algorithm to user-defined coiled-coil sequences. The plot helps visualize the LOGICOIL scores at each position of the coiled-coil sequence.

1 | ```
plot_LOGICOIL(prob.oligo, id)
``` |

`prob.oligo` |
A matrix of dimension n x 4, where n is the length of the input coiled-coil sequence, and each column represents the LOGICOIL scores for antiparallel dimer, parallel, trimer and higher-order coiled coiled. |

`id` |
A string that represents the id name of the input sequence. |

The required input for this function can be obtained by running the `EstimateProbability`

function (see example).

A PNG file that shows the LOGICOIL prediction scores at each of the position of the input coiled-coil sequence.

Thomas L. Vincent tlfvincent@gmail.com

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).

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ```
library(nnet)
data(pssm)
data(Model_Parameters)
data(LOGICOILfit)
cat("Estimating oligomeric state of coiled-coil sequences\n")
prob.oligo <- EstimateProbability("GCN4wt",
"MKQLEDKVEELLSKNYHLENEVARLKKLV",
"abcdefgabcdefgabcdefgabcdefga",
pssm,
LOGICOILfit,
Model_Parameters)
# plot LOGICOIL results obtained from user-defined coiled-coil sequences
plot_LOGICOIL(prob.oligo, "GCN4wt")
``` |

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