R/allGenerics.R

In spliceSites: A bioconductor package for exploration of alignment gap positions from RNA-seq data

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##  File   : allGenerics.r                                                   ##
##  Date   : 28.Okt.2012                                                     ##
##  Content: Generics declarations for package spliceSites                   ##
##  Version: 0.7.0                                                           ##
##  Author : W. Kaisers                                                      ##
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setGeneric("seqid",           function(x) standardGeneric("seqid"))
setGeneric("start",           function(x) standardGeneric("start"))
setGeneric("end",             function(x) standardGeneric("end"))
setGeneric("id",              function(x) standardGeneric("id"))
setGeneric("count",           function(x) standardGeneric("count"))
setGeneric("seqnames",        function(x) standardGeneric("seqnames"))

setGeneric("lCodons",         function(x, frame = 1, keepStrand = TRUE)
                                    standardGeneric("lCodons"))

setGeneric("rCodons",         function(x, frame = 1L, keepStrand = TRUE)
                                standardGeneric("rCodons"))

setGeneric("lrCodons",        function(x, frame = 1L, strand = "+")
                                standardGeneric("lrCodons"))

setGeneric("dnaRanges",       function(x, dnaset, useStrand = TRUE,
        removeUnknownStrand = TRUE, verbose = TRUE, ...)
            standardGeneric("dnaRanges"))

setGeneric("truncateSeq",     function(x, rme = TRUE, trunc = 42L)
                                standardGeneric("truncateSeq"))

setGeneric("trypsinCleave",   function(x, minLen = 5, ...)
                                standardGeneric("trypsinCleave"))


setGeneric("dnaGapSites",     function(x, dnaset, featlen = 3, gaplen = 8,
                                    strand) standardGeneric("dnaGapSites"))

setGeneric("extractRange",    function(object, seqid, start, end)
                                    standardGeneric("extractRange"))

setGeneric("seqlogo",         function(x, strand = "+", useStrand = TRUE, ...)
                                standardGeneric("seqlogo"))


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## Basic accessors
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setGeneric("seqid" ,          function(x) standardGeneric("seqid"))
setGeneric("lstart",          function(x) standardGeneric("lstart"))
setGeneric("lend"  ,          function(x) standardGeneric("lend"))
setGeneric("rstart",          function(x) standardGeneric("rstart"))
setGeneric("rend"  ,          function(x) standardGeneric("rend"))
setGeneric("gptm",            function(x) standardGeneric("gptm"))
setGeneric("rpmg",            function(x) standardGeneric("rpmg"))
setGeneric("getProfile",      function(x) standardGeneric("getProfile"))
setGeneric("getSequence",     function(x) standardGeneric("getSequence"))

setGeneric("trim_left" ,      function(x,maxlen) standardGeneric("trim_left"))
setGeneric("trim_right",      function(x,maxlen) standardGeneric("trim_right"))
setGeneric("resize_left",     function(x,len) standardGeneric("resize_left"))
setGeneric("resize_right",    function(x,len) standardGeneric("resize_right"))


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## Alternative sites
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setGeneric("alt_left_ranks" ,  function(x) standardGeneric("alt_left_ranks"))
setGeneric("alt_right_ranks" , function(x) standardGeneric("alt_right_ranks"))

setGeneric("alt_ranks",       function(object) standardGeneric("alt_ranks"))


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## Junction Sites
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setGeneric("lJunc",          function(x, featlen, gaplen, unique = FALSE,
                                    strand, ...)
                                    standardGeneric("lJunc"))

setGeneric("rJunc",          function(x, featlen, gaplen, unique = FALSE,
                                    strand, ...) standardGeneric("rJunc"))

setGeneric("lrJunc",         function(x, lfeatlen, rfeatlen, strand, ...)
                                    standardGeneric("lrJunc"))

setGeneric("lJuncStrand",    function(x, featlen, gaplen, ...)
                                    standardGeneric("lJuncStrand"))

setGeneric("rJuncStrand",    function(x, featlen, gaplen, ...)
                                    standardGeneric("rJuncStrand"))

setGeneric("lrJuncStrand",   function(x, lfeatlen, rfeatlen, ...)
                                    standardGeneric("lrJuncStrand"))

setGeneric("annotate",       function(object, junc) standardGeneric("annotate"))
setGeneric("getAnnStrand",   function(object) standardGeneric("getAnnStrand"))
setGeneric("addGeneAligns",  function(x) standardGeneric("addGeneAligns"))
setGeneric("sortTable",      function(x) standardGeneric("sortTable"))


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## write.files
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setGeneric("write.files",    function(x, path, filename, ...)
                                        standardGeneric("write.files"))


setGeneric("write.annDNA.tables", function(object, dnaset, filename,
            featlen = 3, gaplen = 8, sep = ";", dec = ".", row.names = FALSE)
            standardGeneric("write.annDNA.tables"))


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## plot Distance between lend and left_end and between rstart and right_start
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setGeneric("plot_diff",		function(x,n=20) standardGeneric("plot_diff"))
setGeneric("plot_diff_ranks",	function(x) standardGeneric("plot_diff_ranks"))


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## Generics for keyProfiler
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setGeneric("addKeyTable",  function(object, keyTable, index, values)
                            standardGeneric("addKeyTable"))
setGeneric("getKeyTable", function(object) standardGeneric("getKeyTable"))
setGeneric("appendKeyTable", function(object, keytable, prefix, valFactor,
                                rateFactor, digits)
                                standardGeneric("appendKeyTable"))


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## Generics for maxEntScore
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setGeneric("saveMaxEnt",	function(object,filename,...) standardGeneric("saveMaxEnt"))
setGeneric("score5",		function(x,seq,pos,...) standardGeneric("score5"))
setGeneric("score3",		function(x,seq,pos,which="ent",...) standardGeneric("score3"))
setGeneric("addMaxEnt",		function(x,dna,maxent,digits=1) standardGeneric("addMaxEnt"))
setGeneric("setMeStrand",	function(x) standardGeneric("setMeStrand"))
setGeneric("getMeStrand",	function(x) standardGeneric("getMeStrand"))
setGeneric("scoreSeq5",		function(x,seq,frame) standardGeneric("scoreSeq5"))
setGeneric("scoreSeq3",		function(x,seq,frame,which="ent",...) standardGeneric("scoreSeq3"))


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## Generics for hbond Score
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setGeneric("hbond",		function(x,seq,pos,...) standardGeneric("hbond"))
setGeneric("addHbond",		function(x,dna) standardGeneric("addHbond"))


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## Generics for ExpressionSet
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setGeneric("uniqueJuncAnn",
        function(object, junc, ann=TRUE, ...) standardGeneric("uniqueJuncAnn"))

# Add Annotation, MaxEnt and Junction sequences
# -> featureData in ExpressionSet
setGeneric("addGenomeData",
           function(object, dna, junc) standardGeneric("addGenomeData"))

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## Generic for plotting
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setGeneric("plotGeneAlignDepth",
        function(reader, genome, gene=NULL, transcript=NULL,
                    log="y", cex.main=2,
                    col="grey50", fill="grey90", grid=TRUE,
                    box.col="grey20", box.border="grey80")
        standardGeneric("plotGeneAlignDepth"))


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## Generics provided by packages on which spliceSites depends on:
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## Provided by IRanges >=1.18.2
## setGeneric("width",           function(x) standardGeneric(("width"))
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## Provided by Biostrings >=2.28.0
## setGeneric("translate",      function(x) standardGeneric(("translate"))
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## Provided by BiocGenerics >=0.6.0
## setGeneric("annotation",   function(object) standardGeneric(("annotation"))
## setGeneric("annotation<-", function(object,value)
##                               standardGeneric("annotation<-"))
## setGeneric("strand",       function(x,...) standardGeneric(("strand"))
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## Provided by rbamtools (specialized for gapSites)
## setGeneric("nAligns",         function(object) standardGeneric(("nAligns"))
## setGeneric("nAlignGaps",      function(object) standardGeneric(("nAlignGaps"))
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## Provided by refGenome (specialized for maxEntScore)
## setGeneric("basedir",function(object) standardGeneric(("basedir"))
## setGeneric("basedir<-",function(object,value) standardGeneric(("basedir<-"))
## setGeneric("extractByGeneName",function(object,geneNames,src,...)
##               standardGeneric("extractByGeneName"))
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## END OF FILE
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