Dear All,

I have a RangedDataList which has many duplicated IRanges. I would like to have a unique set from the original IRanges. I was trying to use the "unique" function, by IRanges::unique (see below), but somehow it was still called from the base. Is there a way to access the unique function, or some other functions I can use to get a unique set of the original IRanges? Thanks.

-Kunbin


> search()
 [1] ".GlobalEnv"            "package:ShortRead"     "package:Rsamtools"
 [4] "package:lattice"       "package:Biostrings"    "package:GenomicRanges"
 [7] "package:IRanges"       "package:stats"         "package:graphics"
[10] "package:grDevices"     "package:utils"         "package:datasets"
[13] "package:methods"       "Autoloads"             "package:base"
> ls(7)
  [1] "active"                         "active<-"
  [3] "aggregate"                      "append"
  [5] "applyFun"                       "applyFun<-"
  [7] "applyParams"                    "applyParams<-"
  [9] "as.data.frame"                  "as.env"
 [11] "as.factor"                      "as.list"
 [13] "as.matrix"                      "asNormalIRanges"
 [15] "as.table"                       "as.vector"
 [17] "Binning"                        "by"
 [19] "cbind"                          "CharacterList"
 [21] "chartr"                         "collapse"
 [23] "colnames"                       "colnames<-"
 [25] "complete.cases"                 "ComplexList"
 [27] "cor"                            "countOverlap"
[29] "countOverlaps"                  "cov"
 [31] "coverage"                       "coverage.normargWidth"
 [33] "DataFrame"                      "DataFrameList"
 [35] "desc"                           "desc<-"
 [37] "diff"                           "disjoin"
 [39] "disjointBins"                   "duplicated"
 [41] "Dups"                           "elementLengths"
 [43] "elementMetadata"                "elementMetadata<-"
 [45] "elementType"                    "end"
 [47] "end<-"                          "endoapply"
 [49] "eval"                           "Filter"
 [51] "filterRules"                    "filterRules<-"
 [53] "FilterRules"                    "Find"
 [55] "findOverlaps"                   "findRange"
 [57] "findRun"                        "flank"
 [59] "follow"                         "gaps"
 [61] "grouplength"                    "grouprank"
 [63] "gsub"                           "H2LGrouping"
 [65] "head"                           "high2low"
 [67] "%in%"                           "IntegerList"
 [69] "intersect"                      "IntervalTree"
 [71] "IQR"                            "IRanges"
 [73] "IRangesList"                    "isConstant"
 [75] "isDisjoint"                     "isEmpty"
 [77] "isNormal"                       "isSingleInteger"
 [79] "isSingleIntegerOrNA"            "isSingleNumber"
 [81] "isSingleNumberOrNA"             "isSingleString"
 [83] "isSingleStringOrNA"             "isTRUEorFALSE"
 [85] "is.unsorted"                    "lapply"
 [87] "levels"                         "LogicalList"
[89] "low2high"                       "mad"
 [91] "Map"                            "mapply"
 [93] "Mask"                           "MaskCollection.show_frame"
 [95] "maskedratio"                    "maskedwidth"
 [97] "match"                          "matchMatrix"
 [99] "mean"                           "median"
[101] "members"                        "mendoapply"
[103] "metadata"                       "metadata<-"
[105] "mid"                            "na.exclude"
[107] "na.omit"                        "narrow"
[109] "nchar"                          "ncol"
[111] "NCOL"                           "nearest"
[113] "new2"                           "newViews"
[115] "ngap"                           "nir_list"
[117] "nlevels"                        "nobj"
[119] "normargShift"                   "normargWeight"
[121] "nrow"                           "NROW"
[123] "nrun"                           "NumericList"
[125] "order"                          "overlap"
[127] "PartitioningByEnd"              "PartitioningByWidth"
[129] "paste"                          "pgap"
[131] "pintersect"                     "pmax"
[133] "pmax.int"                       "pmin"
[135] "pmin.int"                       "Position"
[137] "precede"                        "psetdiff"
[139] "punion"                         "quantile"
[141] "queryHits"                      "rangedData"
[143] "rangedData<-"                   "RangedData"
[145] "RangedDataList"                 "RangedSelection"
[147] "ranges"                         "ranges<-"
[149] "RangesList"                     "rank"
[151] "RawList"                        "rbind"
[153] "rdapply"                        "RDApplyParams"
[155] "read.agpMask"                   "read.gapMask"
[157] "read.liftMask"                  "read.rmMask"
[159] "read.trfMask"                   "reduce"
[161] "Reduce"                         "reducerFun"
[163] "reducerFun<-"                   "reducerParams"
[165] "reducerParams<-"                "reflect"
[167] "rep.int"                        "resize"
[169] "restrict"                       "rev"
[171] "reverse"                        "Rle"
[173] "RleList"                        "RleViewsList"
[175] "rownames"                       "rownames<-"
[177] "runLength"                      "runLength<-"
[179] "runmean"                        "runmed"
[181] "runq"                           "runsum"
[183] "runValue"                       "runValue<-"
[185] "runwtsum"                       "safeExplode"
[187] "sapply"                         "score"
[189] "score<-"                        "sd"
[191] "seqselect"                      "seqselect<-"
[193] "setdiff"                        "setValidity2"
[195] "SharedRaw"                      "SharedRaw.read"
[197] "SharedRaw.readComplexes"        "SharedRaw.readInts"
[199] "SharedRaw.write"                "SharedRaw.writeInts"
[201] "SharedVector.compare"           "SharedVector.copy"
[203] "shift"                          "shiftApply"
[205] "SimpleList"                     "simplify"
[207] "simplify<-"                     "slice"
[209] "smoothEnds"                     "solveUserSEW"
[211] "solveUserSEW0"                  "sort"
[213] "space"                          "split"
[215] "SplitDataFrameList"             "splitRanges"
[217] "start"                          "start<-"
[219] "strsplitAsListOfIntegerVectors" "sub"
[221] "subject"                        "subjectHits"
[223] "subseq"                         "subseq<-"
[225] "subset"                         "subsetByOverlaps"
[227] "substr"                         "substring"
[229] "subviews"                       "successiveIRanges"
[231] "successiveViews"                "summary"
[233] "svn.time"                       "t"
[235] "table"                          "tail"
[237] "tapply"                         "threebands"
[239] "togroup"                        "togrouplength"
[241] "togrouprank"                    "tolower"
[243] "toString"                       "toupper"
[245] "trim"                           "union"
[247] "unique"                         "universe"
[249] "universe<-"                     "unlist"
[251] "update"                         "updateObject"
[253] "values"                         "values<-"
[255] "var"                            "viewApply"
[257] "viewMaxs"                       "viewMeans"
[259] "viewMins"                       "viewRangeMaxs"
[261] "viewRangeMins"                  "Views"
[263] "viewSums"                       "viewWhichMaxs"
[265] "viewWhichMins"                  "vmembers"
[267] "which"                          "whichAsIRanges"
[269] "whichFirstNotNormal"            "width"
[271] "width<-"                        "window"
[273] "window<-"                       "with"
[275] "XDouble"                        "XInteger"
[277] "XNumeric"                       "XRaw"
[279] "xtabs"                          "xvcopy"
> IRanges::unique
standardGeneric for "unique" defined from package "base"

function (x, incomparables = FALSE, ...)
standardGeneric("unique")
<environment: 0x1a51db98>
Methods may be defined for arguments: x, incomparables
Use  showMethods("unique")  for currently available ones.
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-linux-gnu

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] ShortRead_1.6.2     Rsamtools_1.0.1     lattice_0.19-11
[4] Biostrings_2.16.7   GenomicRanges_1.0.1 IRanges_1.6.8

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2   tools_2.11.0
>


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