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 |