Hello,
I get a problem when I build up my GRangesList element by element.
e.g.
> gRangesList <- GRangesList()
> load("C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/22-02-2010/s_8_1/PrEC_INPUT_1_GR.Rdata")
> #loads object called 'rs'
> head(rs)
GRanges with 6 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [ 482, 482] - |
[2] chr1 [ 637, 637] - |
[3] chr1 [4818, 4818] - |
[4] chr1 [6322, 6322] - |
[5] chr1 [7375, 7375] - |
[6] chr1 [9138, 9138] - |
seqlengths
chr1 chr10 chr11 chr12 chr13 chr14 chr15
chr16 chr17 chr18 ... chr3 chr4 chr5 chr6 chr7
chr8 chr9 chrM chrX chrY
247249719 135374737 134452384 132349534 114142980 106368585 100338915
88827254 78774742 76117153 ... 199501827 191273063 180857866 170899992
158821424 146274826 140273252 16571 154913754 57772954
> gRangesList[[1]] <- rs
> load("C:/Users/dario/Documents/Garvan/rawData/seq/Ramaciotti/25-03-2010/s_8_1/LNCaP_INPUT_1_GR.Rdata")
> # loads another object called 'rs'
> head(rs)
GRanges with 6 ranges and 0 elementMetadata values
seqnames ranges strand |
<Rle> <IRanges> <Rle> |
[1] chr1 [ 277, 277] - |
[2] chr1 [ 6163, 6163] - |
[3] chr1 [ 7357, 7357] - |
[4] chr1 [45011, 45011] - |
[5] chr1 [48676, 48676] - |
[6] chr1 [48945, 48945] - |
seqlengths
chr1 chr10 chr11 chr12 chr13 chr14 chr15
chr16 chr17 chr18 ... chr3 chr4 chr5 chr6 chr7
chr8 chr9 chrM chrX chrY
247249719 135374737 134452384 132349534 114142980 106368585 100338915
88827254 78774742 76117153 ... 199501827 191273063 180857866 170899992
158821424 146274826 140273252 16571 154913754 57772954
> gRangesList[[2]] <- rs
>
> endoapply(gRangesList, resize, seqLen)
Error in validObject(.Object) :
invalid class "GRangesList" object: number of rows in non-NULL
'elementMetadata(x)' must match length of 'x'
Whereas, using the GRangesList constructor is problem free :
> gr1 <-
+ GRanges(seqnames = "chr2", ranges = IRanges(3, 6),
+ strand = "+", score = 5L, GC = 0.45)
> gr2 <-
+ GRanges(seqnames = c("chr1", "chr1"),
+ ranges = IRanges(c(7,13), width = 3),
+ strand = c("+", "-"), score = 3:4, GC = c(0.3, 0.5))
> gr3 <-
+ GRanges(seqnames = c("chr1", "chr2"),
+ ranges = IRanges(c(1, 4), c(3, 9)),
+ strand = c("-", "-"), score = c(6L, 2L), GC = c(0.4, 0.1))
> grl <- GRangesList("gr1" = gr1, "gr2" = gr2, "gr3" = gr3)
> xtnd <- endoapply(grl, resize, seqLen)
> sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-pc-mingw32
locale:
[1] LC_COLLATE=English_Australia.1252 LC_CTYPE=English_Australia.1252
LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
LC_TIME=English_Australia.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg18_1.3.16 DNAcopy_1.22.0
chipseq_0.4.0 ShortRead_1.6.2
Rsamtools_1.0.0
[6] lattice_0.18-8 BSgenome_1.16.0
Biostrings_2.16.0 GenomicRanges_1.0.9
IRanges_1.6.17
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.1 hwriter_1.2 tools_2.11.1
--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia
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