narrowpeaks profMatrix rangeval error
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Robert Chase ▴ 10
@robert-chase-6534
Last seen 8.3 years ago
Hello ChIPSeq Analysts, I am trying to use the narrowpeaks vignette available below to create narrowpeaks files from my macs-output-wig-file for a ChIPSeq experiment. http://www.bioconductor.org/packages/release/bioc/vignettes/NarrowPeak s/inst/doc/NarrowPeaks.pdf I would like to incorporate this into a pipeline eventually. I appear to create a candidates data structure without error, but when I try to run the narrowpeaks function I get a rangeval error in the fpca function. It looks like nrow(profMatrix) == 1 and the code is expecting the end of the range to be higher. Any help would be appreciated, -Rob > library(NarrowPeaks) Loading required package: splines No methods found in "GenomicRanges" for requests: unique > wigScores <- wig2CSARScore(wigfilename="NA_treat_afterfiting_chr1.wig", nbchr = 1, chrle = c(30427671)) READING [ NA_treat_afterfiting_chr1.wig ] : done -NB_Chr = 1 -Summary : | chr1 | 10 | 30427671 | CREATING BINARY FILES [CSAR Bioconductor pkg format] : - chr1 : done > print(wigScores$infoscores$filenames) [1] "chr1_ChIPseq.CSARScore" > library(CSAR) Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: ‘BiocGenerics’ The following objects are masked from ‘package:parallel’: clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following object is masked from ‘package:stats’: xtabs The following objects are masked from ‘package:base’: anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, duplicated, eval, evalq, Filter, Find, get, intersect, is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff, sort, table, tapply, union, unique, unlist Loading required package: GenomicRanges Loading required package: XVector > candidates <- sigWin(experiment=wigScores@infoscores, t=1.0,g=30) Error in sigWin(experiment = wigScores@infoscores, t = 1, g = 30) : trying to get slot "infoscores" from an object of a basic class ("list") with no slots > candidates <- sigWin(experiment=wigScores$infoscores, t=1.0,g=30) chr1 done... > head(candidates) GRanges with 6 ranges and 2 metadata columns: seqnames ranges strand | posPeak score <rle> <iranges> <rle> | <numeric> <numeric> [1] chr1 [10171, 10300] * | 10201 5 [2] chr1 [10351, 10460] * | 10361 3 [3] chr1 [12031, 12100] * | 12031 2 [4] chr1 [12131, 12140] * | 12131 2 [5] chr1 [12171, 12380] * | 12211 6 [6] chr1 [13251, 13500] * | 13401 4 --- seqlengths: chr1 30427671 > shortpeaksP0 <-narrowpeaks(inputReg=candidates, scoresInfo = wigScores$infoscores, lmin=0, nbf=25, rpenalty=0, nderiv=0, npcomp=2, pv=80, pmaxscor=0.0, ms=0) Error in create.bspline.basis(rangeval = c(1, nrow(profMatrix)), nbasis = K, : rangeval[1] must be less than rangeval[2]; instead rangeval[1] = 1 rangeval[2] = 1 In addition: There were 50 or more warnings (use warnings() to see the first 50) > traceback() 4: stop("rangeval[1] must be less than rangeval[2]; instead ", "rangeval[1] = ", rangeval[1], c("==", ">")[diff(rangeval) < 0], " rangeval[2] = ", rangeval[2]) 3: create.bspline.basis(rangeval = c(1, nrow(profMatrix)), nbasis = K, norder = 4) 2: fpca(profiles = binding_profiles_extended, numberOfComponents = npcomp, K = nbf, nderiv = nderiv, lambda = rpenalty) 1: narrowpeaks(inputReg = candidates, scoresInfo = wigScores$infoscores, lmin = 0, nbf = 25, rpenalty = 0, nderiv = 0, npcomp = 2, pv = 80, pmaxscor = 0, ms = 0) [[alternative HTML version deleted]]
ChIPSeq chipseq NarrowPeaks ChIPSeq chipseq NarrowPeaks • 662 views
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