[BioC] Passing multiple files to pdInfobuilder

Andrew Beggs [guest] guest at bioconductor.org
Wed Oct 31 12:47:48 CET 2012


I have multiple pair files from a Nimblegen methylation array that I have converted to XYS files. I am trying to feed them into pdInfobuilder using the script below, but it crashes out with the following error:

Error in validObject(.Object) : 
  invalid class “ScalarCharacter” object: ScalarCharacter must have length one

Does this mean that pdInfobuilder can only take one file at a time? I thought that as the file was being read into an array it could analyse multiple files



baseDir <- "/mnt/cdrive/Nimblegen/methylationpercentages"
ndf <- list.files(baseDir, pattern = ".ndf",full.names = TRUE)
xys <- list.files(baseDir, pattern = ".xys",full.names = TRUE)
pos <- list.files(baseDir, pattern = ".pos",full.names = TRUE)
seed <- new("NgsTilingPDInfoPkgSeed",ndfFile = ndf, xysFile = xys, posFile = pos, author = "Andrew Beggs", email = "a.beggs at bham.ac.uk", biocViews = "AnnotationData",genomebuild = "HG 18", organism = "Human", species = "Homo Sapiens", url = "http://www.biostat.jhsph.edu/~bcarvalh")
makePdInfoPackage(seed, destDir = ".")

 -- output of sessionInfo(): 

R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pdInfoBuilder_1.22.0 oligo_1.22.0         oligoClasses_1.20.0 
[4] affxparser_1.30.0    RSQLite_0.11.2       DBI_0.2-5           
[7] Biobase_2.18.0       BiocGenerics_0.4.0  

loaded via a namespace (and not attached):
 [1] affyio_1.26.0         BiocInstaller_1.8.3   Biostrings_2.26.2    
 [4] bit_1.1-9             codetools_0.2-8       ff_2.2-9             
 [7] foreach_1.4.0         GenomicRanges_1.10.3  IRanges_1.16.3       
[10] iterators_1.0.6       parallel_2.15.2       preprocessCore_1.20.0
[13] splines_2.15.2        stats4_2.15.2         tools_2.15.2         
[16] zlibbioc_1.4.0  

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