Supervised detection of conserved motifs in DNA sequences


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Documentation for package ‘cosmo’ version 1.22.0

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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-method Class "constraintSet" ~~~
plot-method Class "cosmo"
plot-method Class "intInfo" ~~~
plot-method Class "postProbs"
posFreqCon Class "posFreqCon" ~~~
posFreqCon-class Class "posFreqCon" ~~~
postProbs-class Class "postProbs"
print-method Class "align"
print-method Class "constraintSet" ~~~
print-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-method Class "align"
show-method Class "constraintSet" ~~~
show-method Class "cosmo"
simScore Score motif detection simulation results
subMotifCon Class "subMotifCon" ~~~
subMotifCon-class Class "subMotifCon" ~~~
summary-method Class "align"
summary-method Class "cosmo"
transMats Example transition matrix in list format
writeConFile Converts an object of class 'constraintSet' into a text file