[BioC] minfi: Problem with GenomicMethylSet

[Gustavo Fernández Bayón]

Hi everybody.

After upgrading to R3.0 and Bioc 2.13, some of my scripts broke. 
Currently I have a problem that I'll try to reproduce here with a 
minimal scenario:

I have a MethylSet produced by preprocessSWAN.

 > mset
MethylSet (storageMode: lockedEnvironment)
assayData: 485512 features, 20 samples
   element names: Meth, Unmeth
phenoData
   sampleNames: 8691803020_R03C02 8691803043_R02C01 ...
     8691803052_R05C02 (20 total)
   varLabels: Sample_Name Sample_Well ... filenames (22 total)
   varMetadata: labelDescription
Annotation
   array: IlluminaHumanMethylation450k
   annotation: ilmn.v1.2
Preprocessing
   Method: SWAN (based on a MethylSet preprocesses as 'Raw (no 
normalization or bg correction)'
   minfi version: 1.7.3
   Manifest version: 0.4.0

If I try to extract Meth and Unmeth matrices, and create a 
GenomicMethylSet from them, I get the following error:

 > gmset <- GenomicMethylSet(hm450[featureNames(mset)], getMeth(mset),
                           getUnmeth(mset), pData(mset), annotation(mset),
                           preprocessMethod(mset))

Error en GenomicRanges:::.ShallowSimpleListAssays$new :
   objeto de tipo 'closure' no es subconjunto
(Sorry for the Spanish. It is the "object of type closure is not 
subsettable" error)

hm450 is a GRanges object containing an annotation of Illumina 450k probes

 > hm450
GRanges with 485577 ranges and 17 metadata columns:
              seqnames               ranges strand   | addressA addressB 
channel
                 <Rle>            <IRanges> <Rle>   |    <Rle>    
<Rle>   <Rle>
   cg13869341     chr1       [15865, 15866]      *   | 62703328 
16661461     Red
   cg14008030     chr1       [18827, 18828]      *   | 27651330 <NA>    Both
   cg12045430     chr1       [29407, 29408]      *   | 25703424 
34666387     Red
   cg20826792     chr1       [29425, 29426]      *   | 61731400 
14693326     Red
   cg00381604     chr1       [29435, 29436]      *   | 26752380 
50693408     Red
          ...      ...                  ...    ... ...      ... ...     ...
   cg17939569     chrY [27009430, 27009431]      *   | 73757458 <NA>    Both
   cg13365400     chrY [27210334, 27210335]      *   | 61745505 <NA>    Both
   cg21106100     chrY [28555536, 28555537]      *   | 56793430 <NA>    Both
   cg08265308     chrY [28555550, 28555551]      *   | 67794346 
26610401     Red
   cg14273923     chrY [28555912, 28555913]      *   | 16749405 <NA>    Both
              probeType platform percentGC
                  <Rle>    <Rle> <numeric>
   cg13869341        cg    HM450      0,68
   cg14008030        cg    HM450      0,62
   cg12045430        cg    HM450      0,80
   cg20826792        cg    HM450      0,82
   cg00381604        cg    HM450      0,80
          ...       ...      ...       ...
   cg17939569        cg    HM450      0,42
   cg13365400        cg    HM450      0,44
   cg21106100        cg    HM450      0,66
   cg08265308        cg    HM450      0,68
   cg14273923        cg    HM450      0,48
                                                       sourceSeq
<DNAStringSet>
   cg13869341 CCGGTGGCTGGCCACTCTGCTAGAGTCCATCCGCCAAGCTGGGGGCATCG
   cg14008030 CGGGGAACTGCCCCTGCACATACTGAACGGCTCACTGAGCAAACCCCGAG
   cg12045430 GGGGAGGGCGCAGTGGAGGGCGAGCGGCGGCGTTAGGACCCGGAGGCGCG
   cg20826792 CGCCGCCGCTCGCCCTCCACTGCGCCCTCCCCGAGCGCGGCTCCAGGACC
   cg00381604 CGCCCTCCACTGCGCCCTCCCCGAGCGCGGCTCCAGGACCCCGTCGACCC
          ... ...          ...
   cg17939569 CGCCTAAATAAGAATAGGAGTAAAGGAGAGTATTACCTCCAAATCACCGG
   cg13365400 CGTCACCTGGATGCTGGTTTAAGTGATATATGAAAATCCACCCTAAGGAC
   cg21106100 CGGATCTTTCTGACCAGCCCCGGCCCCATCTTGGCCTTACCTGGCCTCCC
   cg08265308 CGGCTCCCAACGCTCGGATCTTTCTGACCAGCCCCGGCCCCATCTTGGCC
   cg14273923 TGGTATTGGTGAAGTCTACCACTCCAGCTCGTAGACTTCCATAATCGTCG
   ---
   seqlengths:
         chr1      chr2      chr3      chr4 ...     chr22 chrX      chrY
    249250621 243199373 198022430 191154276 ...  51304566 155270560 59373566

The problem seems to be located at the following line of code inside the 
GenomicMethylSet constructor:

 > GenomicMethylSet
function (gr, Meth, Unmeth, pData, annotation, preprocessMethod)
{
     assays <- SimpleList(Meth = Meth, Unmeth = Unmeth)
***--->>    assays <- GenomicRanges:::.ShallowSimpleListAssays$new(data 
= assays) <<<---*****
     colData <- as(pData, "DataFrame")
     rowData <- as(gr, "GRanges")
     new("GenomicMethylSet", assays = assays, colData = colData,
         rowData = rowData, annotation = annotation, preprocessMethod = 
preprocessMethod)
}
<environment: namespace:minfi>

and my sessionInfo is the following:

 > sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] es_ES.UTF-8

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

other attached packages:
  [1] IlluminaHumanMethylation450kmanifest_0.4.0
  [2] xlsx_0.5.1
  [3] xlsxjars_0.5.0
  [4] rJava_0.9-4
  [5] genefilter_1.43.0
  [6] minfi_1.7.3
  [7] Biostrings_2.29.3
  [8] GenomicRanges_1.13.13
  [9] XVector_0.1.0
[10] IRanges_1.19.8
[11] reshape_0.8.4
[12] plyr_1.8
[13] lattice_0.20-15
[14] Biobase_2.21.2
[15] BiocGenerics_0.7.2

loaded via a namespace (and not attached):
  [1] annotate_1.39.0       AnnotationDbi_1.23.11 beanplot_1.1
  [4] DBI_0.2-7             grid_3.0.0 illuminaio_0.3.0
  [7] limma_3.17.12         MASS_7.3-26 matrixStats_0.8.1
[10] mclust_4.1            multtest_2.17.0 nor1mix_1.1-4
[13] preprocessCore_1.23.0 RColorBrewer_1.0-5 R.methodsS3_1.4.2
[16] RSQLite_0.11.3        siggenes_1.35.0 splines_3.0.0
[19] stats4_3.0.0          survival_2.37-4 tools_3.0.0
[22] XML_3.96-1.1          xtable_1.7-1

I'm suspicious about the whole updating thing, but I have not been able 
to spot if there is a package which is not updated properly.

Any help would be much appreciated.

Regards,
Gus