Ok Brad, after your cry for help on another forum I have spent some
more
time and I are now able to reproduce your problem (the fact I could
not
reproduce it earlier, was entirely my fault I now realize). I will
try to
submit a fix tonight, and will report back here when it is done.
Sorry for
the trouble.
Best,
Kasper
On Wed, Jun 11, 2014 at 10:50 AM, Ruzicka, William B.,M.D. <
wruzicka@mclean.harvard.edu> wrote:
> Hi Kasper -
> Thanks for your help.
> I've upgraded to R-3.1.0 but bumphunter is still giving the same
"unused
> aregument" error:
>
>
>
> > sessionInfo()
>
> R version 3.1.0 (2014-04-10)
>
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>
>
> locale:
>
> [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
> States.1252
>
> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
>
>
> [5] LC_TIME=English_United States.1252
>
>
>
> attached base packages:
>
> [1] parallel stats graphics grDevices utils datasets
methods
> base
>
>
>
> other attached packages:
>
> [1] doParallel_1.0.8
> IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
>
> [3] IlluminaHumanMethylation450kmanifest_0.4.0 minfi_1.10.1
>
>
> [5] bumphunter_1.4.2
locfit_1.5-9.1
>
>
> [7] iterators_1.0.7
foreach_1.4.2
>
>
> [9] Biostrings_2.32.0
XVector_0.4.0
>
>
> [11] GenomicRanges_1.16.3
GenomeInfoDb_1.0.2
>
>
> [13] IRanges_1.22.8
lattice_0.20-29
>
>
> [15] Biobase_2.24.0
> BiocGenerics_0.10.0
>
>
>
> loaded via a namespace (and not attached):
>
> [1] annotate_1.42.0 AnnotationDbi_1.26.0 base64_1.1
> beanplot_1.1
>
> [5] codetools_0.2-8 compiler_3.1.0 DBI_0.2-7
> digest_0.6.4
>
> [9] doRNG_1.6 genefilter_1.46.1 grid_3.1.0
> illuminaio_0.6.0
>
> [13] limma_3.20.4 MASS_7.3-33 matrixStats_0.10.0
> mclust_4.3
>
> [17] multtest_2.20.0 nlme_3.1-117 nor1mix_1.1-4
> pkgmaker_0.22
>
> [21] plyr_1.8.1 preprocessCore_1.26.1 R.methodsS3_1.6.1
> RColorBrewer_1.0-5
>
> [25] Rcpp_0.11.2 registry_0.2 reshape_0.8.5
> rngtools_1.2.4
>
> [29] RSQLite_0.11.4 siggenes_1.38.0 splines_3.1.0
> stats4_3.1.0
>
> [33] stringr_0.6.2 survival_2.37-7 tools_3.1.0
> XML_3.98-1.1
>
> [37] xtable_1.7-3 zlibbioc_1.10.0
>
>
>
> > traceback()
>
> 10: stop(simpleError(msg, call = expr))
>
> 9: e$fun(obj, substitute(ex), parent.frame(), e$data)
>
> 8: list(args = iter(IndexesChunks)(.doRNG.stream = list(c(407L,
>
> -631507724L, 2080869221L, 1065599202L, 1311698683L, -323805696L,
>
> -1040906751L), c(407L, 1945611946L, -608207003L, 1842430237L,
>
> -518903442L, 1824620966L, -1548636643L), c(407L, 237898474L,
>
> 1062912735L, -1334786133L, 1059436525L, 793963592L, 1493198629L
>
> ), c(407L, 1527452477L, -1461135650L, 1252537885L, 1975038170L,
>
> -892552789L, -512077693L))), argnames = c("idx", ".doRNG.stream"
>
> ), evalenv = <environment>, specified = character(0), combineInfo
= list(
>
> fun = function (a, ...)
>
> c(a, list(...)), in.order = TRUE, has.init = TRUE, init =
list(),
>
> final = NULL, multi.combine = TRUE, max.combine = 100),
errorHandling = "stop",
>
> packages = c("bumphunter", "doRNG"), export = NULL, noexport
= NULL,
>
> options = list(), verbose = FALSE) %dopar% {
>
> {
>
> rngtools::RNGseed(.doRNG.stream)
>
> }
>
> {
>
> sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster =
cluster[idx],
>
> weights = weights[idx, ], verbose = verbose, ...)
>
> c(sm, list(idx = idx))
>
> }
>
> }
>
> 7: do.call("%dopar%", list(obj, ex), envir = parent.frame())
>
> 6: foreach(idx = iter(IndexesChunks), .packages = "bumphunter")
%dorng%
>
> {
>
> sm <- smoothFunction(y = y[idx, ], x = x[idx], cluster =
cluster[idx],
>
> weights = weights[idx, ], verbose = verbose, ...)
>
> c(sm, list(idx = idx))
>
> }
>
> 5: smoother(y = rawBeta, x = pos, cluster = cluster, weights =
weights,
>
> smoothFunction = smoothFunction, verbose = subverbose, ...)
>
> 4: bumphunterEngine(getMethSignal(object, type), design = design,
>
> chr = as.factor(seqnames(object)), pos = start(object),
cluster = cluster,
>
> coef = coef, cutoff = cutoff, cutoffQ = cutoffQ, maxGap =
maxGap,
>
> smooth = smooth, smoothFunction = smoothFunction, useWeights
= useWeights,
>
> B = B, verbose = verbose, ...)
>
> 3: .local(object, ...)
>
> 2: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B =
100,
>
> maxGap = 500, smooth = TRUE, smoothFunction =
locfitByCluster)
>
> 1: bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE, B =
100,
>
> maxGap = 500, smooth = TRUE, smoothFunction =
locfitByCluster)
>
>
>
> R version 3.1.0 (2014-04-10) -- "Spring Dance"
>
> Copyright (C) 2014 The R Foundation for Statistical Computing
>
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
>
>
> R is free software and comes with ABSOLUTELY NO WARRANTY.
>
> You are welcome to redistribute it under certain conditions.
>
> Type 'license()' or 'licence()' for distribution details.
>
>
>
> R is a collaborative project with many contributors.
>
> Type 'contributors()' for more information and
>
> 'citation()' on how to cite R or R packages in publications.
>
>
>
> Type 'demo()' for some demos, 'help()' for on-line help, or
>
> 'help.start()' for an HTML browser interface to help.
>
> Type 'q()' to quit R.
>
>
>
> [Workspace loaded from ~/.RData]
>
>
>
> > require(minfi)
>
> Loading required package: minfi
>
> Loading required package: BiocGenerics
>
> Loading required package: parallel
>
>
>
> Attaching package: æ
iocGenerics?
>
> The following objects are masked from æackage:parallel?
>
>
>
> clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply,
>
> parCapply, parLapply, parLapplyLB, parRapply, parSapply,
parSapplyLB
>
>
>
> The following object is masked from æackage:stats?
>
>
>
> xtabs
>
>
>
> The following objects are masked from æackage:base?
>
>
>
> anyDuplicated, append, as.data.frame, as.vector, cbind,
colnames, do.call, 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: Biobase
>
> Welcome to Bioconductor
>
>
>
> Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor,
>
> see 'citation("Biobase")', and for packages
'citation("pkgname")'.
>
>
>
> Loading required package: lattice
>
> Loading required package: GenomicRanges
>
> Loading required package: IRanges
>
> Loading required package: GenomeInfoDb
>
> Loading required package: Biostrings
>
> Loading required package: XVector
>
> Loading required package: bumphunter
>
> Loading required package: foreach
>
> foreach: simple, scalable parallel programming from Revolution
Analytics
>
> Use Revolution R for scalability, fault tolerance and more.
>
>
http://www.revolutionanalytics.com
>
> Loading required package: iterators
>
> Loading required package: locfit
>
> locfit 1.5-9.1 2013-03-22
>
> > setwd("G:/Illumina/Brad/Minfi")
>
> > baseDir <- "G:/Illumina/Brad/Minfi/Scan Output"
>
> > targets <- read.450k.sheet(baseDir)
>
> [read.450k.sheet] Found the following CSV files:
>
> [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv"
>
> > RGSet <- read.450k.exp(base = baseDir, targets = targets)
>
> > pd <- pData(RGSet)
>
> > pd[,1:4]
>
> Sample_Name Sample_Well Sample_Plate Sample_Group
>
> 8942300007_R02C01 CON1_CA32 B01 Plate1 CON_CA32
>
> 8942300010_R06C01 CON2_CA32 B01 Plate1 CON_CA32
>
> 8942297078_R06C01 CON3_CA32 F02 Plate1 CON_CA32
>
> 8942300010_R01C01 CON4_CA32 E02 Plate1 CON_CA32
>
> 8942300010_R05C01 CON5_CA32 A01 Plate1 CON_CA32
>
> 8942297143_R06C02 CON6_CA32 H02 Plate1 CON_CA32
>
> 8942297143_R06C01 CON7_CA32 B02 Plate1 CON_CA32
>
> 8942297143_R01C02 CON8_CA32 C02 Plate1 CON_CA32
>
> 8942300007_R01C01 SZ1_CA32 A01 Plate1 SZ_CA32
>
> 8942300007_R03C01 SZ2_CA32 C01 Plate1 SZ_CA32
>
> 8942297078_R03C02 SZ3_CA32 A01 Plate1 SZ_CA32
>
> 8942300010_R02C01 SZ4_CA32 F02 Plate1 SZ_CA32
>
> 8942300010_R02C02 SZ5_CA32 D01 Plate1 SZ_CA32
>
> 8942297078_R01C01 SZ6_CA32 A02 Plate1 SZ_CA32
>
> 8942297143_R04C01 SZ7_CA32 H01 Plate1 SZ_CA32
>
> 8942297078_R06C02 SZ8_CA32 D01 Plate1 SZ_CA32
>
> >
>
> > gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers =
TRUE, removeBadSamples = TRUE, badSampleCutoff = 10.5,
quantileNormalize = TRUE, stratified = TRUE, mergeManifest = FALSE,
sex = NULL)
>
> [preprocessQuantile] Mapping to genome.
>
> Loading required package: IlluminaHumanMethylation450kmanifest
>
> Loading required package:
IlluminaHumanMethylation450kanno.ilmn12.hg19
>
> [preprocessQuantile] Fixing outliers.
>
> [preprocessQuantile] Quantile normalizing.
>
> >
>
> > GADBroad <- read.csv("GAD1LessBroad.csv")
>
> > GRSGADBroad <- as.vector(GADBroad)
>
> > Test <- GADBroad[1:1856,1]
>
> > MSetGADBroad <- as.vector(GADBroad[,1])
>
> > GRQ <- gRatioSet.quantile[Test]
>
> > diagnosis <- pData(gRatioSet.quantile)$diagnosis
>
> > designMatrix <- model.matrix(~ diagnosis)
>
> > library(doParallel)
>
> > registerDoParallel(cores = 4)
>
> > dmrs <- bumphunter(GRQ, design = designMatrix, pickCutoff = TRUE,
B=100, maxGap=500, smooth=TRUE, smoothFunction=locfitByCluster)
>
> [bumphunterEngine] Parallelizing using 4 workers/cores (backend:
doParallelSNOW, version: 1.0.8).
>
> [bumphunterEngine] Computing coefficients.
>
> [bumphunterEngine] Smoothing coefficients.
>
> Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)"
>
>
> - Brad
>
> ------------------------------
> *From:* kasperdanielhansen@gmail.com [kasperdanielhansen@gmail.com]
on
> behalf of Kasper Daniel Hansen [khansen@jhsph.edu]
> *Sent:* Tuesday, June 10, 2014 9:48 PM
> *To:* Brad Ruzicka [guest]
> *Cc:* bioconductor@r-project.org; Ruzicka, William B.,M.D.
> *Subject:* Re: [BioC] smoothing function in bumphunter in minfi
>
> I have been prompted on this off-list. Turns out I was reading
the OP
> a bit too fast ... he is on R 3.0.3 which we no longer support (nor
can I
> make changes to the relevant Bioconductor packages). So the
solution is to
> upgrade to R-3.1.
>
> Hopefully that will fix the problem, otherwise get in touch.
Whatever I
> have done would not have affected R 3.0.3.
>
> Best,
> Kasper
>
>
> On Wed, May 14, 2014 at 11:31 AM, Kasper Daniel Hansen
<khansen@jhsph.edu>
> wrote:
>
>> This is a weirdly introduced error which we have fixed in the devel
>> branch. I was supposed to back port it into release, but I forgot.
>>
>> Kasper
>>
>>
>> On Wed, May 14, 2014 at 11:16 AM, Brad Ruzicka [guest] <
>> guest@bioconductor.org> wrote:
>>
>>> Hi there-
>>> I've been using bumphunter within minfi to analyze my HM450
dataset with
>>> good results, but I'm unable to use the smoothing function within
>>> bumphunter. When "smooth = TRUE" it gives the error:
>>> "Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)"",
even
>>> though I have not included cutoffQ in the script.
>>>
>>> The script below works fine with smooth = FALSE, but when set to
true
>>> gives the above error:
>>>
>>> setwd("G:/Illumina/Brad/Minfi")
>>> baseDir <- "G:/Illumina/Brad/Minfi/Scan Output"
>>> targets <- read.450k.sheet(baseDir)
>>> RGSet <- read.450k.exp(base = baseDir, targets = targets)
>>> pd <- pData(RGSet)
>>> pd[,1:4]
>>>
>>> gRatioSet.quantile <- preprocessQuantile(RGSet, fixOutliers =
TRUE,
>>> removeBadSamples = TRUE, badSampleCutoff = 10.5, quantileNormalize
= TRUE,
>>> stratified = TRUE, mergeManifest = FALSE, sex = NULL)
>>>
>>> Age <- pData(gRatioSet.quantile)$age
>>> PMI <- pData(gRatioSet.quantile)$PMI
>>> diagnosis <- pData(gRatioSet.quantile)$diagnosis
>>> gender <- pData(gRatioSet.quantile)$gender
>>>
>>> designMatrix <- model.matrix(~ diagnosis + Age + PMI + gender)
>>>
>>> library(doParallel)
>>> registerDoParallel(cores = 4)
>>> dmrs <- bumphunter(gRatioSet.quantile, design = designMatrix,
>>> maxGap=500, pickCutoff = TRUE, smooth = TRUE,
>>> smoothFunction=locfitByCluster, B=1000)
>>> write.csv(dmrs$table, file = "GAD1BroadDMRsSZ3Test6.csv")
>>>
>>> Output of script:
>>> [read.450k.sheet] Found the following CSV files:
>>> [1] "G:/Illumina/Brad/Minfi/Scan Output/SampleSheetSZ32.csv"
>>> [preprocessQuantile] Mapping to genome.
>>> [preprocessQuantile] Fixing outliers.
>>> [preprocessQuantile] Quantile normalizing.
>>> [bumphunterEngine] Parallelizing using 4 workers/cores (backend:
>>> doParallelSNOW, version: 1.0.8).
>>> [bumphunterEngine] Computing coefficients.
>>> [bumphunterEngine] Smoothing coefficients.
>>> Error in { : task 1 failed - "unused argument (cutoffQ = 0.99)"
>>>
>>> Any ideas where my error is?
>>> Thanks,
>>> Brad
>>>
>>> -- output of sessionInfo():
>>>
>>> > sessionInfo()
>>> R version 3.0.3 (2014-03-06)
>>> Platform: x86_64-w64-mingw32/x64 (64-bit)
>>>
>>> locale:
>>> [1] LC_COLLATE=English_United States.1252
>>> [2] LC_CTYPE=English_United States.1252
>>> [3] LC_MONETARY=English_United States.1252
>>> [4] LC_NUMERIC=C
>>> [5] LC_TIME=English_United States.1252
>>>
>>> attached base packages:
>>> [1] parallel stats graphics grDevices utils datasets
methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] doParallel_1.0.8
>>> [2] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
>>> [3] IlluminaHumanMethylation450kmanifest_0.4.0
>>> [4] doRNG_1.6
>>> [5] rngtools_1.2.4
>>> [6] pkgmaker_0.20
>>> [7] registry_0.2
>>> [8] minfi_1.8.9
>>> [9] bumphunter_1.2.0
>>> [10] locfit_1.5-9.1
>>> [11] iterators_1.0.7
>>> [12] foreach_1.4.2
>>> [13] Biostrings_2.30.1
>>> [14] GenomicRanges_1.14.4
>>> [15] XVector_0.2.0
>>> [16] IRanges_1.20.7
>>> [17] reshape_0.8.5
>>> [18] lattice_0.20-29
>>> [19] Biobase_2.22.0
>>> [20] BiocGenerics_0.8.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] annotate_1.40.1 AnnotationDbi_1.24.0 base64_1.1
>>> [4] beanplot_1.1 codetools_0.2-8 compiler_3.0.3
>>> [7] DBI_0.2-7 digest_0.6.4 genefilter_1.44.0
>>> [10] grid_3.0.3 illuminaio_0.4.0 itertools_0.1-3
>>> [13] limma_3.18.13 MASS_7.3-33
matrixStats_0.8.14
>>> [16] mclust_4.3 multtest_2.18.0 nlme_3.1-117
>>> [19] nor1mix_1.1-4 plyr_1.8.1
preprocessCore_1.24.0
>>> [22] R.methodsS3_1.6.1 RColorBrewer_1.0-5 Rcpp_0.11.1
>>> [25] RSQLite_0.11.4 siggenes_1.36.0 splines_3.0.3
>>> [28] stats4_3.0.3 stringr_0.6.2 survival_2.37-7
>>> [31] tools_3.0.3 XML_3.98-1.1 xtable_1.7-3
>>>
>>> --
>>> Sent via the guest posting facility at bioconductor.org.
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor@r-project.org
>>>
https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>>
http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>
>>
>
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