[BioC] smoothing function in bumphunter in minfi

[Brad Ruzicka [guest]]

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 

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