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
>
______________________________________________________________________
The contents of this electronic message, including any attachments, are
intended only for the use of the individual or entity to which they are
addressed and may contain confidential information. If you are not the intended
recipient, you are hereby notified that any use, dissemination, distribution,
or copying of this message or any attachment is strictly prohibited. If you
have received this transmission in error, please send an e-mail to
[email protected] and delete this message, along with any
attachments, from your computer.
[[alternative HTML version deleted]]
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
