krm: Kernel Based Regression Models
Version 2016.7-9

Implements several methods for testing the variance component parameter in regression models that contain kernel-based random effects, including a maximum of adjusted scores test. Several kernels are supported, including a profile hidden Markov model mutual information kernel for protein sequence.

AuthorYouyi Fong <youyifong@gmail.com>, Saheli Datta, Krisztian Sebestyen
Date of publication2016-07-10 11:55:52
MaintainerYouyi Fong <youyifong@gmail.com>
LicenseGPL-2
Version2016.7-9
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("krm")

Popular man pages

aa.prop.list: Amino Acid Properties
chi.norm: A Transformation of Chi-squared Random Variable
krm: Kernel-based Regression Models
krm.score.test: Adjusted Score Test
profile_HMM: Functions related to profile HMM
seq_read_write: Read a Fasta Sequence File
sim.liu: Simulate sDataset
See all...

All man pages Function index File listing

Man pages

aa.prop.list: Amino Acid Properties
chi.norm: A Transformation of Chi-squared Random Variable
cloud9: 9-Component Mixture Dirichlet Prior for Protein Sequences
dirichlet_functions: Functions related to mixture Dirichlet distribution
getSeqKernel: Protein Sequence Kernels
krm: Kernel-based Regression Models
krm.most: Kernel-based Regression Model Maximum of adjusted Score Test
krm.score.test: Adjusted Score Test
profile_HMM: Functions related to profile HMM
seq_alignment: Functions Related to Sequence Alignment
seq_read_write: Read a Fasta Sequence File
sim.liu: Simulate sDataset

Functions

E.QQ Source code
aa.prop.list Man page
aa2arabic Man page Source code
alignment2count Man page Source code
alignment2trancount Man page Source code
arabic2arabicFile Man page Source code
arabic2fastaFile Man page Source code
calcPairwiseIdentity Man page Source code
chi.norm Man page Source code
cloud9 Man page
ddirichlet Man page Source code
dmdirichlet Man page Source code
fastaFile2arabicFile Man page Source code
getSeqKernel Man page Source code
hmmMargLlik Man page Source code
krm Man page
krm.most Man page Source code
krm.score.test Man page Source code
logIntegrateDirichlet Man page Source code
logIntegrateMixDirichlet Man page Source code
modifyDirichlet Man page Source code
my.lbeta Source code
perturbation.test Source code
rdirichlet Man page Source code
readArabicFile Man page Source code
readBlockFile Man page Source code
readFastaFile Man page Source code
readPriorFromFile Man page Source code
readSelexAsMatrix Man page Source code
readSelexFile Man page Source code
removeGap Man page Source code
rmdirichlet Man page Source code
selexFile2arabicFile Man page Source code
sim.liu.2007 Man page Source code
sim.liu.2008 Man page Source code
string2arabic Man page Source code
stringList2arabicFile Man page Source code
varQ Source code
writeFastaFile Man page Source code

Files

inst
inst/misc
inst/misc/sim1.fasta
inst/misc/y1.txt
inst/misc/SETpfamseed_aligned_for_testing.fasta
inst/unitTests
inst/unitTests/runRUnitTests.R
inst/unitTests/Makefile
inst/unitTests/runit.krm.score.test.R
inst/unitTests/report.txt
inst/unitTests/runit.getSeqKernel.R
inst/unitTests/runit.krm.most.R
tests
tests/doRUnit.R
src
src/Makevars
src/DirichletRV.h
src/Observable.h
src/MI_kernel.cpp
src/StatPlus.h
src/MixtureDirichletRV.h
src/score_var.cpp
src/MathPlus.h
src/MixtureDirichletRV.cpp
src/ProteinSequence.cpp
src/DirichletRV.cpp
src/ProteinSequence.h
src/rvgs.h
src/RandomPlus.h
src/U.h
src/rvgs.cpp
src/Makevars.win
src/var_Q.cpp
NAMESPACE
data
data/cloud9.rda
data/aa.prop.list.rda
R
R/dirichlet_functions.R
R/EQQ.R
R/krm.score.test.R
R/sim.liu.R
R/seq_read_write.R
R/profile_HMM.R
R/krm.most.R
R/getSeqKernel.r
R/misc.R
R/seq_alignment.R
MD5
DESCRIPTION
ChangeLog
man
man/getSeqKernel.Rd
man/chi.norm.Rd
man/krm.score.test.Rd
man/aa.prop.list.Rd
man/seq_alignment.Rd
man/sim.liu.Rd
man/cloud9.Rd
man/krm.Rd
man/krm.most.Rd
man/dirichlet_functions.Rd
man/profile_HMM.Rd
man/seq_read_write.Rd
krm documentation built on May 19, 2017, 4:39 p.m.

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