# Software Package for Transcription Factor Binding Site (TFBS) Analysis

## Documentation for package ‘TFBSTools’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E G I L M N P R S T V W X misc

## -- A --

as.data.frame-method | Class '"SitePairSet"'
as.data.frame-method | Class '"SitePairSetList"'
as.data.frame-method | Class '"SiteSet"'
as.data.frame-method | Class '"SiteSetList"'
as.matrix-method | '"XMatrix"' objects

## -- B --

bg | '"XMatrix"' objects
bg-method | '"XMatrix"' objects
bg-method | Class '"XMatrixList"'
bg<--method | '"XMatrix"' objects

## -- C --

c-method | Class '"SiteSet"'
c-methods | Class '"SiteSet"'
calConservation | calConservation method
calConservation-method | calConservation method
calConservation-methods | calConservation method
colSums-method | '"XMatrix"' objects
consensusMatrix-method | Class '"MotifSet"'

## -- D --

deleteMatrixHavingID | JASPAR database operations
deleteMatrixHavingID-method | JASPAR database operations
dim-method | '"XMatrix"' objects
dmmEM | dmmEM method
dmmEM-method | dmmEM method
dmmEM-methods | dmmEM method

## -- E --

end-method | Class '"SiteSet"'

## -- G --

getEmissionProb | Get the emission distribution parameters.
getEmissionProb-method | Get the emission distribution parameters.
getMatrixByID | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixByID-method | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixByName | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixByName-method | Basic JASPAR database search functionis 'getMatrixByID', 'getMatrixByName'
getMatrixSet | Advanced JASPAR database search functions 'get_MatrixSet'
getMatrixSet-method | Advanced JASPAR database search functions 'get_MatrixSet'
getPosProb | Get the emission probabilities of nucleotides
getPosProb-method | Get the emission probabilities of nucleotides

## -- I --

ICMatrix | '"XMatrix"' objects
ICMatrix-class | '"XMatrix"' objects
ICMatrixList | Class '"XMatrixList"'
ICMatrixList-class | Class '"XMatrixList"'
ID | '"XMatrix"' objects
ID-method | '"XMatrix"' objects
ID-method | Class '"XMatrixList"'
ID<--method | '"XMatrix"' objects
initializeJASPARDB | JASPAR database operations
initializeJASPARDB-method | JASPAR database operations
IUPAC2Matrix | IUPAC2Matrix

## -- L --

length-method | Class '"MotifSet"'
length-method | Class '"SitePairSet"'
length-method | Class '"SiteSet"'
length-method | '"XMatrix"' objects
length-methods | '"XMatrix"' objects

## -- M --

MA0003.2 | Some example PFM matrices.
MA0004.1 | Some example PFM matrices.
MA0043 | Some example PFM matrices.
MA0048 | Some example PFM matrices.
makeFlatFileDir | Generate "FlatFileDir" directory
Matrix | '"XMatrix"' objects
Matrix-method | '"XMatrix"' objects
Matrix-method | Class '"XMatrixList"'
Matrix<- | '"XMatrix"' objects
Matrix<--method | '"XMatrix"' objects
matrixClass | '"XMatrix"' objects
matrixClass-method | '"XMatrix"' objects
matrixClass-method | Class '"XMatrixList"'
matrixClass<--method | '"XMatrix"' objects
matrixType | '"XMatrix"' objects
matrixType-method | '"XMatrix"' objects
matrixType-method | Class '"XMatrixList"'
matrixType-methods | '"XMatrix"' objects
MotifSet | Class '"MotifSet"'
MotifSet-class | Class '"MotifSet"'

## -- N --

name | '"XMatrix"' objects
name-method | '"XMatrix"' objects
name-method | Class '"XMatrixList"'
name<--method | '"XMatrix"' objects
ncol-method | The TFFM class
ncol-method | '"XMatrix"' objects

## -- P --

parseMEMEOutput | parseMEMEOutput
pattern-method | Class '"SiteSet"'
permuteMatrix | permuteMatrix method
permuteMatrix-method | permuteMatrix method
permuteMatrix-methods | permuteMatrix method
PFMatrix | '"XMatrix"' objects
PFMatrix-class | '"XMatrix"' objects
PFMatrixList | Class '"XMatrixList"'
PFMatrixList-class | Class '"XMatrixList"'
PFMSimilarity | PFMSimilarity method
PFMSimilarity-method | PFMSimilarity method
PFMSimilarity-methods | PFMSimilarity method
primary-method | Class '"SiteSet"'
pvalues | Class '"SiteSet"'
pvalues-method | Class '"SiteSet"'
pvalues-method | Class '"SiteSetList"'
PWMatrix | '"XMatrix"' objects
PWMatrix-class | '"XMatrix"' objects
PWMatrixList | Class '"XMatrixList"'
PWMatrixList-class | Class '"XMatrixList"'
PWMSimilarity | PWMSimilarity method
PWMSimilarity-method | PWMSimilarity method
PWMSimilarity-methods | PWMSimilarity method

## -- R --

readJASPARMatrix | Read JASPAR format matrix
readXMLTFFM | readXMLTFFM
relScore | Class '"SiteSet"'
relScore-method | Class '"SiteSet"'
relScore-method | Class '"SiteSetList"'
reverseComplement-method | '"XMatrix"' objects
rowSums-method | '"XMatrix"' objects
rPWMDmm | rPWMDmm method
rPWMDmm-method | rPWMDmm method
rPWMDmm-methods | rPWMDmm method
runMEME | Wrapper function for MEME
runMEME-method | Wrapper function for MEME

## -- S --

sampleRanges | sampleRanges
score-method | Class '"SiteSet"'
searchAln | searchAln method
searchAln-method | searchAln method
searchPairBSgenome | searchPairBSgenome method
searchPairBSgenome-method | searchPairBSgenome method
searchPairBSgenome-methods | searchPairBSgenome method
searchSeq | searchSeq method
searchSeq-method | searchSeq method
searchSeq-methods | searchSeq method
seqLogo | Plot a sequence logo
seqLogo-method | Plot a sequence logo
seqname-method | Class '"SiteSet"'
shannon.entropy | Calculate the Shannon entropy
show-method | Class '"SiteSet"'
showAsCell-method | Class '"XMatrixList"'
site1-method | Class '"SitePairSet"'
site2-method | Class '"SitePairSet"'
SitePairSet | Class '"SitePairSet"'
SitePairSet-class | Class '"SitePairSet"'
SitePairSetList | Class '"SitePairSetList"'
SitePairSetList-class | Class '"SitePairSetList"'
SiteSet | Class '"SiteSet"'
SiteSet-class | Class '"SiteSet"'
SiteSetList | Class '"SiteSetList"'
SiteSetList-class | Class '"SiteSetList"'
sitesource-method | Class '"SiteSet"'
sitesSeq | Class '"MotifSet"'
sitesSeq-method | Class '"MotifSet"'
start-method | Class '"SiteSet"'
storeMatrix | JASPAR database operations
storeMatrix-method | JASPAR database operations
storeMatrix-methods | JASPAR database operations
strand-method | Class '"SiteSet"'
strand-method | '"XMatrix"' objects
strand-method | Class '"XMatrixList"'
strand<--method | '"XMatrix"' objects

## -- T --

tags | '"XMatrix"' objects
tags-method | '"XMatrix"' objects
tags-method | Class '"XMatrixList"'
TFBSTools | TFBS software package.
TFFM | The TFFM class
TFFMDetail | The TFFM class
TFFMFirst | The TFFM class
toGRangesList | toGRangesList function
toGRangesList-method | toGRangesList function
toGRangesList-methods | toGRangesList function
toICM | toICM method
toICM-method | toICM method
toPWM | toPWM method
toPWM-method | toPWM method
totalIC | '"XMatrix"' objects
totalIC-method | The TFFM class
totalIC-method | '"XMatrix"' objects
totalIC-methods | '"XMatrix"' objects

## -- V --

views | Class '"SiteSet"'
views-method | Class '"SiteSet"'

## -- W --

writeGFF2 | 'writeGFF3', 'writeGFF2' functions
writeGFF2-method | 'writeGFF3', 'writeGFF2' functions
writeGFF2-methods | 'writeGFF3', 'writeGFF2' functions
writeGFF3 | 'writeGFF3', 'writeGFF2' functions
writeGFF3-method | 'writeGFF3', 'writeGFF2' functions
writeGFF3-methods | 'writeGFF3', 'writeGFF2' functions

## -- X --

XMatrix | '"XMatrix"' objects
XMatrix-class | '"XMatrix"' objects
XMatrixList | Class '"XMatrixList"'
XMatrixList-method | Class '"XMatrixList"'

## -- misc --

[-method | Class '"MotifSet"'
[-method | Class '"SiteSet"'
[-methods | '"XMatrix"' objects