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## Accessors
setGeneric("ID", signature="x", function(x)
standardGeneric("ID"))
setGeneric("ID<-", signature="x", function(x, value)
standardGeneric("ID<-"))
setGeneric("name", signature="x", function(x)
standardGeneric("name"))
setGeneric("name<-", signature="x", function(x, value)
standardGeneric("name<-"))
setGeneric("matrixClass", signature="x", function(x)
standardGeneric("matrixClass"))
setGeneric("matrixClass<-", signature="x", function(x, value)
standardGeneric("matrixClass<-"))
setGeneric("Matrix", signature="x", function(x)
standardGeneric("Matrix"))
setGeneric("Matrix<-", signature="x", function(x, value)
standardGeneric("Matrix<-"))
setGeneric("bg", signature="x", function(x)
standardGeneric("bg"))
setGeneric("bg<-", signature="x", function(x, value)
standardGeneric("bg<-"))
setGeneric("tags", signature="x", function(x)
standardGeneric("tags"))
setGeneric("matrixType", signature="x", function(x)
standardGeneric("matrixType"))
setGeneric("pseudocounts", signature="x", function(x)
standardGeneric("pseudocounts"))
setGeneric("pseudocounts<-", signature="x", function(x, value)
standardGeneric("pseudocounts<-"))
setGeneric("schneider", signature="x", function(x)
standardGeneric("schneider"))
setGeneric("schneider<-", signature="x", function(x, value)
standardGeneric("schneider<-"))
setGeneric("views", signature="x", function(x)
standardGeneric("views"))
setGeneric("seqname", signature="x", function(x)
standardGeneric("seqname"))
setGeneric("sitesource", signature="x", function(x)
standardGeneric("sitesource"))
setGeneric("primary", signature="x", function(x)
standardGeneric("primary"))
setGeneric("siteset1", signature="x", function(x)
standardGeneric("siteset1"))
setGeneric("siteset2", signature="x", function(x)
standardGeneric("siteset2"))
setGeneric("alignments", signature="x", function(x)
standardGeneric("alignments"))
setGeneric("conservation1", signature="x", function(x)
standardGeneric("conservation1"))
setGeneric("seqlength", signature="x", function(x)
standardGeneric("seqlength"))
setGeneric("alnlength", signature="x", function(x)
standardGeneric("alnlength"))
setGeneric("seqname1", signature="x", function(x)
standardGeneric("seqname1"))
setGeneric("seqname2", signature="x", function(x)
standardGeneric("seqname2"))
## Constructors
setGeneric("XMatrixList", signature="x",
function(x, use.names=TRUE, ...)
standardGeneric("XMatrixList")
)
## JASPAR DB
setGeneric("getMatrixByID", signature="x", function(x, ID)
standardGeneric("getMatrixByID"))
setGeneric("getMatrixByName", signature="x", function(x, name)
standardGeneric("getMatrixByName"))
setGeneric("getMatrixSet", signature="x", function(x, opts)
standardGeneric("getMatrixSet"))
setGeneric("storeMatrix",
function(x, pfmList) standardGeneric("storeMatrix")
)
setGeneric("initializeJASPARDB", signature="x",
function(x, version=c("2014", "2016", "2018"))
standardGeneric("initializeJASPARDB"))
setGeneric("deleteMatrixHavingID", signature="x",
function(x, IDs) standardGeneric("deleteMatrixHavingID"))
## PFM,PWM, ICM
#setGeneric("colSums", signature="x",
# function(x) standardGeneric("colSums"))
setGeneric("toICM", signature="x",
function(x, pseudocounts=0.8, schneider=FALSE,
bg=c(A=0.25, C=0.25, G=0.25, T=0.25))
standardGeneric("toICM")
)
setGeneric("toPWM", signature="x",
function(x, type=c("log2probratio", "prob"), pseudocounts=0.8,
bg=c(A=0.25, C=0.25, G=0.25, T=0.25))
standardGeneric("toPWM")
)
#setGeneric("plotLogo", signature="x",
# function(x, ic.scale = TRUE, xaxis = TRUE, yaxis = TRUE,
# xfontsize = 15, yfontsize = 15) standardGeneric("plotLogo")
# )
setGeneric("seqLogo", signature="x",
function(x, ic.scale = TRUE, xaxis = TRUE, yaxis = TRUE,
xfontsize = 15, yfontsize = 15) standardGeneric("seqLogo")
)
setGeneric("totalIC", signature="x",
function(x) standardGeneric("totalIC"))
setGeneric("searchSeq", #signature="x",
function(x, subject, seqname="Unknown", strand="*", min.score="80%",
mc.cores=1L)
standardGeneric("searchSeq"))
setGeneric("searchAln",
function(pwm, aln1, aln2, seqname1="Unknown1", seqname2="Unknown2",
min.score="80%", windowSize=51L, cutoff=0.7,
strand="*", type="any", conservation=NULL, mc.cores=1L)
standardGeneric("searchAln")
)
setGeneric("toGRangesList", function(x, axt)
standardGeneric("toGRangesList"))
setGeneric("doSiteSearch",
function(pwm, aln1, aln2, min.score="80%", windowSize=51L,
cutoff=0.7,
strand="*", conservation=NULL)
standardGeneric("doSiteSearch")
)
setGeneric("searchPairBSgenome", signature="pwm",
function(pwm, BSgenome1, BSgenome2, chr1, chr2,
min.score="80%", strand="*", chain)
standardGeneric("searchPairBSgenome")
)
setGeneric("calConservation",
function(aln1, aln2, windowSize=51L, which="1")
standardGeneric("calConservation")
)
### SiteSet methods
setGeneric("writeGFF3", signature="x",
function(x, scoreType=c("absolute", "relative"))
standardGeneric("writeGFF3"))
setGeneric("writeGFF2", signature="x",
function(x, scoreType=c("absolute", "relative"))
standardGeneric("writeGFF2"))
setGeneric("relScore", signature="x", function(x)
standardGeneric("relScore"))
setGeneric("pvalues", signature="x",
function(x, type=c("TFMPvalue", "sampling"))
standardGeneric("pvalues"))
setGeneric("clone", signature="x", function(x, ...)
standardGeneric("clone"))
## PWM methods
setGeneric("PWMSimilarity",
function(pwmSubject, pwmQuery,
method=c("Euclidean", "Pearson", "KL"))
standardGeneric("PWMSimilarity"))
## PFM methods
setGeneric("PFMSimilarity",
function(pfmSubject, pfmQuery, openPenalty=3, extPenalty=0.01)
#max.results=10, min.percent_score=NULL, min.score=NULL)
standardGeneric("PFMSimilarity"))
setGeneric("permuteMatrix", signature="x",
function(x, type="intra") standardGeneric("permuteMatrix"))
setGeneric("dmmEM", signature="x",
function(x, K=6, alg=c("C", "R"))
standardGeneric("dmmEM"))
setGeneric("rPWMDmm", signature="x",
function(x,alpha0, pmix, N=1, W=6)
standardGeneric("rPWMDmm"))
## wrappers
setGeneric("runMEME", signature="x",
function(x, binary="meme", seqtype="DNA",
arguments=list(), tmpdir=tempdir())
standardGeneric("runMEME"))
setGeneric("sitesSeq", signature="x",
function(x, n=10, type="none")
standardGeneric("sitesSeq"))
## TFFM methods
setGeneric("bgEmissionProb", signature="tffm",
function(tffm)
standardGeneric("bgEmissionProb"))
setGeneric("getPosStart", signature="tffm",
function(tffm)
standardGeneric("getPosStart"))
setGeneric("getPosProb", signature="tffm",
function(tffm)
standardGeneric("getPosProb"))
setGeneric("getEmissionProb", signature="tffm",
function(tffm)
standardGeneric("getEmissionProb"))
setGeneric("getTransition", signature="tffm",
function(tffm, i, j)
standardGeneric("getTransition"))
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