ProteinDescriptors: Generates Various Protein Descriptors for Machine Learning Algorithms

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An implementation of protein descriptors in R. These descriptors combine the advantages of being fixed length and including partial sequential effect: Various length of protein sequences are described with fixed length vectors that are suitable for machine learning algorithms, and still includes partial sequential effect.

Author
Berat Kurar [aut, cre], Sami Abu Sneineh [aut], Yaqoub Ashhab [aut]
Date of publication
2016-03-03 23:40:47
Maintainer
Berat Kurar <beratkurar@gmail.com>
License
BSD 3-clause License + file LICENSE
Version
0.1.0

View on CRAN

Man pages

DiscreteBlosum
Discrete blosum descriptor.
DiscreteSequentialBlosumTwoParts
Discrete sequential blosum descriptor with split number=2.
DiscreteSequentialSparseFiveParts
Discrete sequential sparse descriptor with split number=5.
DiscreteSequentialSparseFourParts
Discrete sequential sparse descriptor with split number=4.
DiscreteSequentialSparseThreeParts
Discrete sequential sparse descriptor with split number=3.
DiscreteSequentialSparseTwoParts
Discrete sequential sparse descriptor with split number=2.
DiscreteSequentialTdTwoParts
Discrete sequential 3D descriptor with split number=2.
DiscreteSparse
Discrete sparse descriptor.
DiscreteTd
Discrete 3D descriptor.
IncrementalDiscreteSparse
Incremental discrete sparse descriptor.
LastFirstDiscreteSparse
Last first discrete sparse descriptor.
SequentialBlosum
Sequential blosum descriptor.
SequentialDiscreteBlosum
Sequential discrete blosum descriptor with step size=2.
SequentialDiscreteSparse
Sequential discrete sparse descriptor with step size=2.
SequentialDiscreteTd
Sequential discrete 3D descriptor with step size=2.
SequentialSparse
Sequential sparse descriptor.
SequentialTd
Sequential 3D descriptor.
ShiftedDiscreteSparse
Discrete sparse descriptor.

Files in this package

ProteinDescriptors
ProteinDescriptors/NAMESPACE
ProteinDescriptors/R
ProteinDescriptors/R/DiscreteTd.R
ProteinDescriptors/R/LastFirstDiscreteSparse.R
ProteinDescriptors/R/DiscreteSequentialBlosumTwoParts.R
ProteinDescriptors/R/IncrementalDiscreteSparse.R
ProteinDescriptors/R/SequentialDiscreteBlosum.R
ProteinDescriptors/R/DiscreteSequentialSparseThreeParts.R
ProteinDescriptors/R/DiscreteBlosum.R
ProteinDescriptors/R/ShiftedDiscreteSparse.R
ProteinDescriptors/R/DiscreteSequentialSparseFiveParts.R
ProteinDescriptors/R/SequentialDiscreteSparse.R
ProteinDescriptors/R/DiscreteSequentialSparseFourParts.R
ProteinDescriptors/R/SequentialSparse.R
ProteinDescriptors/R/DiscreteSparse.R
ProteinDescriptors/R/SequentialBlosum.R
ProteinDescriptors/R/DiscreteSequentialTdTwoParts.R
ProteinDescriptors/R/SequentialDiscreteTd.R
ProteinDescriptors/R/DiscreteSequentialSparseTwoParts.R
ProteinDescriptors/R/SequentialTd.R
ProteinDescriptors/MD5
ProteinDescriptors/DESCRIPTION
ProteinDescriptors/man
ProteinDescriptors/man/DiscreteSequentialSparseFiveParts.Rd
ProteinDescriptors/man/SequentialDiscreteTd.Rd
ProteinDescriptors/man/SequentialDiscreteBlosum.Rd
ProteinDescriptors/man/DiscreteSparse.Rd
ProteinDescriptors/man/IncrementalDiscreteSparse.Rd
ProteinDescriptors/man/SequentialDiscreteSparse.Rd
ProteinDescriptors/man/DiscreteTd.Rd
ProteinDescriptors/man/DiscreteBlosum.Rd
ProteinDescriptors/man/SequentialSparse.Rd
ProteinDescriptors/man/DiscreteSequentialSparseTwoParts.Rd
ProteinDescriptors/man/DiscreteSequentialTdTwoParts.Rd
ProteinDescriptors/man/DiscreteSequentialSparseThreeParts.Rd
ProteinDescriptors/man/SequentialTd.Rd
ProteinDescriptors/man/DiscreteSequentialSparseFourParts.Rd
ProteinDescriptors/man/LastFirstDiscreteSparse.Rd
ProteinDescriptors/man/DiscreteSequentialBlosumTwoParts.Rd
ProteinDescriptors/man/SequentialBlosum.Rd
ProteinDescriptors/man/ShiftedDiscreteSparse.Rd
ProteinDescriptors/LICENSE