Entering edit mode
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
