[BioC] Repeat masker sequences as GRanges object

[James W. MacDonald]

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]]
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>



-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

	[[alternative HTML version deleted]]