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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