[BioC] Repeat masker sequences as GRanges object
Hermann Norpois
hnorpois at gmail.com
Mon Sep 15 13:19:58 CEST 2014
Thanks,
I followed your instructions but I got an error message:
library (AnnotationHub)
> hub <- AnnotationHub()
> seq.masked <- hub$goldenpath.hg19.database.rmsk_0.0.1.RData
Retrieving ‘goldenpath/hg19/database/rmsk_0.0.1.RData’
Fehler: Lesefehler aus Verbindung # 'Fehler' means error and 'Verbindung'
connection
But I was able to download the package. So, principally a "connection" is
possible.
sessionInfo ()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=de_DE.UTF-8 LC_NUMERIC=C
[3] LC_TIME=de_DE.UTF-8 LC_COLLATE=de_DE.UTF-8
[5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=de_DE.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] AnnotationHub_1.0.2 GenomicRanges_1.12.5 IRanges_1.18.4
[4] BiocGenerics_0.6.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.22.6 Biobase_2.20.1 BiocInstaller_1.10.4
[4] compiler_3.1.0 DBI_0.3.0 rjson_0.2.14
[7] RSQLite_0.11.4 stats4_3.1.0 tools_3.1.0
Whats wrong with my connection?
Thanks
Hermann
2014-09-12 15:30 GMT+02:00 James W. MacDonald <jmacdon at uw.edu>:
> Hi Hermann,
>
> How about this:
>
> > library(AnnotationHub)
> > hub <- AnnotationHub()
> > hub$goldenpath.hg19.database.rmsk_0.0.1.RData
> GRanges with 5298130 ranges and 2 metadata columns:
> seqnames ranges strand |
> name
> <Rle> <IRanges> <Rle> |
> <character>
> [1] chr1 [16777161, 16777470] + |
> AluSp
> [2] chr1 [25165801, 25166089] - |
> AluY
> [3] chr1 [33553607, 33554646] + |
> L2b
> [4] chr1 [50330064, 50332153] + |
> L1PA10
> [5] chr1 [58720068, 58720973] - |
> L1PA2
> ... ... ... ... ...
> ...
> [5298126] chr21_gl000210_random [25379, 25875] + |
> MER74B
> [5298127] chr21_gl000210_random [26438, 26596] - |
> MIRc
> [5298128] chr21_gl000210_random [26882, 27022] - |
> MIRc
> [5298129] chr21_gl000210_random [27297, 27447] + |
> HAL1-2a_MD
> [5298130] chr21_gl000210_random [27469, 27682] + |
> HAL1-2a_MD
> score
> <numeric>
> [1] 2147
> [2] 2626
> [3] 626
> [4] 12545
> [5] 8050
> ... ...
> [5298126] 1674
> [5298127] 308
> [5298128] 475
> [5298129] 371
> [5298130] 370
> ---
> seqlengths:
> chr1 chr2 ... chr18_gl000207_random
> 249250621 243199373 ... 4262
>
> This is a GRanges of all features from UCSC's Repeat Masker table.
>
> Best,
>
> Jim
>
>
>
>
> On Thu, Sep 11, 2014 at 3:16 AM, Hermann Norpois <hnorpois at gmail.com>
> wrote:
>
>> Hello,
>>
>> I would like to have repeat sequences as GRanges object
>> I started with ...
>>
>> library (BSgenome.Hsapiens.UCSC.hg19)
>> ch1 <- Hsapiens$chr1
>> active (masks (ch1))
>> AGAPS AMB RM TRF
>> TRUE TRUE FALSE FALSE
>> active (masks(ch1))["RM"] <- TRUE
>> active (masks (ch1))
>> AGAPS AMB RM TRF
>> TRUE TRUE TRUE FALSE
>>
>> Can anyboldy give me a hint how to continue.
>>
>> Thanks
>> hermann
>>
>> [[alternative HTML version deleted]]
>>
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>
>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
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