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/NarrowPeaks/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)

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