# Supervised detection of conserved motifs in DNA sequences

## Documentation for package `cosmo' version 1.2.0

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

addCon | Add constraints to an already existing constraint set
align-class | Class "align"
bfile2tmat | Converting a MEME-style background file to a transition matrix
bgModel | Estimating the background Markov model
boundCon | Class "boundCon" ~~~
boundCon-class | Class "boundCon" ~~~
constraintSet-class | Class "constraintSet" ~~~
cosmo | Constrained motif detection main function
cosmo-class | Class "cosmo"
intInfo | Class "intInfo" ~~~
intInfo-class | Class "intInfo" ~~~
license.cosmo | Print cosmo license
makeBoundCon | Constructing a bound constraint
makeConSet | Constructing a constraint set.
makePalCon | Constructing a palindromic constraint
makePosFreqCon | Constructing a nucleotide frequency constraint
makeShapeCon | Constructing a shape constraint
makeShapeDiffCon | Constructing a shape parameter difference constraint
makeSubMotifCon | Constructing a submotif constraint
motifPWM | Example position weight matrix
palCon | Class "palCon" ~~~
palCon-class | Class "palCon" ~~~
plot,constraintSet-method | Class "constraintSet" ~~~
plot,cosmo-method | Class "cosmo"
plot,intInfo-method | Class "intInfo" ~~~
plot,postProbs-method | Class "postProbs"
posFreqCon | Class "posFreqCon" ~~~
posFreqCon-class | Class "posFreqCon" ~~~
postProbs-class | Class "postProbs"
print,align-method | Class "align"
print,constraintSet-method | Class "constraintSet" ~~~
print,cosmo-method | Class "cosmo"
readConFile | Reads in a constraint file.
rseq | Random generation of DNA sequence according to ZOOPS or TCM model
shapeCon | Class "shapeCon" ~~~
shapeCon-class | Class "shapeCon" ~~~
shapeDiffCon | Class "shapeDiffCon" ~~~
shapeDiffCon-class | Class "shapeDiffCon" ~~~
show,align-method | Class "align"
show,constraintSet-method | Class "constraintSet" ~~~
show,cosmo-method | Class "cosmo"
simScore | Score motif detection simulation results
subMotifCon | Class "subMotifCon" ~~~
subMotifCon-class | Class "subMotifCon" ~~~
summary,align-method | Class "align"
summary,cosmo-method | Class "cosmo"
transMats | Example transition matrix in list format
writeConFile | Converts an object of class 'constraintSet' into a text file