SMAP: A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
Version 1.40.0

Functions and classes for DNA copy number profiling of array-CGH data

AuthorRobin Andersson <robin.andersson@lcb.uu.se>
Bioconductor views CopyNumberVariation Microarray TwoChannel
Date of publicationNone
MaintainerRobin Andersson <robin.andersson@lcb.uu.se>
LicenseGPL-2
Version1.40.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("SMAP")

Popular man pages

smap: smap: A Segmental Maximum A Posteriori Approach to Array-CGH...
SMAPHMM: Constructor for "SMAPHMM" objects
SMAPHMM-class: Class "SMAPHMM": A class to manage HMMs for the SMAP package
SMAP-internal: SMAP-internal
SMAPObservations: Constructor for "SMAPObservations" objects
SMAPObservations-class: Class "SMAPObservations": A class to manage microarray...
SMAPProfile-class: Class "SMAPProfile"
See all...

All man pages Function index File listing

Man pages

GBM: Glioblastoma multiforme array CGH data
smap: smap: A Segmental Maximum A Posteriori Approach to Array-CGH...
SMAPHMM: Constructor for "SMAPHMM" objects
SMAPHMM-class: Class "SMAPHMM": A class to manage HMMs for the SMAP package
SMAP-internal: SMAP-internal
SMAPObservations: Constructor for "SMAPObservations" objects
SMAPObservations-class: Class "SMAPObservations": A class to manage microarray...
SMAPProfile-class: Class "SMAPProfile"
SMAPProfiles-class: Class "SMAPProfiles"

Functions

A Man page
A,SMAPHMM-method Man page
A,eta-method Man page
A,grad-method Man page
GBM Man page
HMM Man page
HMM,SMAPProfile-method Man page
P Man page
P,SMAPProfile-method Man page
Phi Man page
Phi,SMAPHMM-method Man page
Phi,eta-method Man page
Phi,grad-method Man page
Pi Man page
Pi,SMAPHMM-method Man page
Pi,eta-method Man page
Pi,grad-method Man page
Q Man page
Q,SMAPProfile-method Man page
Q,SMAPProfiles-method Man page
SMAPHMM Man page Source code
SMAPHMM-class Man page
SMAPObservations Man page Source code
SMAPObservations-class Man page
SMAPProfile Source code
SMAPProfile-class Man page
SMAPProfiles-class Man page
[,SMAPObservations-method Man page
[,SMAPProfile-method Man page
[[<-,SMAPProfiles-method Man page
chromosome Man page
chromosome,SMAPObservations-method Man page
endPosition Man page
endPosition,SMAPObservations-method Man page
eta Source code
gaussparam Source code
grad Source code
initialize,SMAPHMM-method Man page
initialize,SMAPObservations-method Man page
initialize,SMAPProfile-method Man page
initialize,eta-method Man page
initialize,gaussparam-method Man page
initialize,grad-method Man page
name Man page
name,SMAPObservations-method Man page
name,SMAPProfile-method Man page
name,SMAPProfiles-method Man page
noObservations Man page
noObservations,SMAPObservations-method Man page
noStates Man page
noStates,SMAPHMM-method Man page
observations Man page
observations,SMAPProfile-method Man page
observations,SMAPProfiles-method Man page
onLoad Source code
plot,SMAPObservations,missing-method Man page
plot,SMAPProfile,missing-method Man page
plot,SMAPProfiles,missing-method Man page
reporterId Man page
reporterId,SMAPObservations-method Man page
show,SMAPHMM-method Man page
show,SMAPObservations-method Man page
show,SMAPProfile-method Man page
show,SMAPProfiles-method Man page
smap Man page
smap,SMAPHMM,SMAPObservations-method Man page
startPosition Man page
startPosition,SMAPObservations-method Man page
value Man page
value,SMAPObservations-method Man page
value,eta-method Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/methods-GaussParam.R
R/methods-SMAPHMM.R
R/methods-SMAPObservations.R
R/methods-SMAPProfile.R
R/methods-eta.R
R/methods-grad.R
build
build/vignette.rds
data
data/GBM.rda
inst
inst/doc
inst/doc/SMAP.R
inst/doc/SMAP.Rnw
inst/doc/SMAP.pdf
man
man/GBM.Rd
man/SMAP-internal.Rd
man/SMAPHMM-class.Rd
man/SMAPHMM.Rd
man/SMAPObservations-class.Rd
man/SMAPObservations.Rd
man/SMAPProfile-class.Rd
man/SMAPProfiles-class.Rd
man/smap.Rd
src
src/gradient.c
src/gradient.h
src/init.c
src/overlap.c
src/overlap.h
src/prob.c
src/prob.h
src/viterbi.c
src/viterbi.h
vignettes
vignettes/SMAP.Rnw
SMAP documentation built on May 20, 2017, 9:59 p.m.

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