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Reimport with .R suffix

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@128656 bc3139a8-67e5-0310-9ffc-ced21a209358

Wolfgang Kaisers authored on 13/04/2017 15:55:53
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+##                                                                           ##
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+##  Project   :   seqTools                                                   ##
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+##  Created   :   26.August.2013                                             ##
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+##  Author    :   W. Kaisers                                                 ##
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+##  File      :   allGenerics.r                                              ##
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+##  Content   :   All static variables and (not directly object related )    ##
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+##                function declarations                                      ##
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+##                                                                           ##
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Changing Fastqq object structure
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+setGeneric("mergeFastqq", function(lhs, rhs) standardGeneric("mergeFastqq"))
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+setGeneric("meltDownK", function(object, newK) standardGeneric("meltDownK"))
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Preparation for Hierarchical clustering (HC)
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+setGeneric("cbDistMatrix", function(object, nReadNorm = max(nReads(object))) 
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+                  standardGeneric("cbDistMatrix"))
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Slot accessors
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+setGeneric("fileNames",   function(object) standardGeneric("fileNames"))
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+setGeneric("collectTime", function(object) standardGeneric("collectTime"))
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+setGeneric("collectDur", function(object) standardGeneric("collectDur"))
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+setGeneric("getK", function(object) standardGeneric("getK"))
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+setGeneric("nFiles", function(object) standardGeneric("nFiles"))
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+setGeneric("nNnucs", function(object) standardGeneric("nNnucs"))
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+setGeneric("nReads", function(object) standardGeneric("nReads"))
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+setGeneric("maxSeqLen", function(object) standardGeneric("maxSeqLen"))
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+setGeneric("seqLenCount", function(object) standardGeneric("seqLenCount"))
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+setGeneric("nucFreq", function(object, i) standardGeneric("nucFreq"))
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+setGeneric("gcContent", function(object, i) standardGeneric("gcContent"))
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+
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+setGeneric("gcContentMatrix", function(object)
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+                                    standardGeneric("gcContentMatrix"))
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+setGeneric("getGCcontent", function(object) standardGeneric("getGCcontent"))
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+
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+setGeneric("seqLen", function(object) standardGeneric("seqLen"))
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+setGeneric("kmerCount", function(object) standardGeneric("kmerCount"))
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+
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+setGeneric("probeLabel", function(object, label)
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+                                        standardGeneric("probeLabel"))
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+
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+setGeneric("probeLabel<-", function(object, value)
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+                                        standardGeneric("probeLabel<-"))
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+
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+setGeneric("phred", function(object, i) standardGeneric("phred"))
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+
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Retrieving Phred distribution
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+setGeneric("phredQuantiles", function(object, quantiles, i, ...)
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+                                        standardGeneric("phredQuantiles"))
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+
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+setGeneric("plotPhredQuant", function(object, i, main, ...)
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+                                        standardGeneric("plotPhredQuant"))
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+
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+## Global Phred content functions
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+setGeneric("phredDist", function(object, i) standardGeneric("phredDist"))
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+
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+setGeneric("plotPhredDist", function(object, i, maxp=45, col, ...)
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+                                        standardGeneric("plotPhredDist"))
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+
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+setGeneric("propPhred", function(object, greater=30, less=93)
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+                                            standardGeneric("propPhred"))
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+
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+
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+setGeneric("mergedPhred", function(object) standardGeneric("mergedPhred"))
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+
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+setGeneric("mergedPhredQuantiles", function(object, quantiles)
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+                                    standardGeneric("mergedPhredQuantiles"))
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+
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+setGeneric("plotMergedPhredQuant", function(object, main, ...)
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+                                    standardGeneric("plotMergedPhredQuant"))
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Predefined Plot functions
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+setGeneric("plotNucFreq", function(object, i, main, maxx, ...)
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+                                            standardGeneric("plotNucFreq"))
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+
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+setGeneric("plotGCcontent", function(object,main,...)
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+                                        standardGeneric("plotGCcontent"))
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+
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+setGeneric("plotNucCount", function(object, nucs=16, maxx, ...)
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+                                        standardGeneric("plotNucCount"))
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+
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+setGeneric("plotKmerCount",
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+                    function(object, index, mxey, main="K-mer count", ...)
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+                                            standardGeneric("plotKmerCount"))
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+
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Singular Value decomposition based on k-mer counts
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+setGeneric("kmerSvd", function(object) standardGeneric("kmerSvd"))
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+
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+
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## END OF FILE
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##