[BioC] subset GRanges object via ElementMetadata

[Arnaud Amzallag]

test.gr[values(test.gr)$over %in% 2]

works. 

test.gr[values(test.gr)$over == 2] works too if over does not contains NAs.

Arnaud

On Feb 22, 2013, at 10:33 AM, Hermann Norpois wrote:

> Hello,
> 
> I am looking for a method to subset a GRangesObject by means of values (or
> ElementMetadata column), for instance
> over==2.
> 
> How does it work?
> 
> Thanks
> Hermann
> 
> 
>> test.gr
> GRanges with 6 ranges and 3 metadata columns:
>      seqnames           ranges strand |  edensity     epeak      over
>         <Rle>        <IRanges>  <Rle> | <integer> <integer> <integer>
>  [1]     chr1 [713844, 714487]      * |      1000       256         1
>  [2]     chr1 [762136, 763199]      * |      1000       771         2
>  [3]     chr1 [780124, 780289]      * |       519        74         0
>  [4]     chr1 [780533, 780677]      * |       516        68         0
>  [5]     chr1 [781104, 781387]      * |       601       140         0
>  [6]     chr1 [793830, 794396]      * |       610       290         0
>  ---
>  seqlengths:
>    chr1 chr10 chr11 chr12 chr13 chr14 ...  chr6  chr7  chr8  chr9  chrX
> chrY
>      NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA    NA
> NA
>> dput (test.gr)
> new("GRanges"
>    , seqnames = new("Rle"
>    , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12",
> "chr13",
> "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2",
> "chr20", "chr21", "chr22", "chr3", "chr4", "chr5", "chr6", "chr7",
> "chr8", "chr9", "chrX", "chrY"), class = "factor")
>    , lengths = 6L
>    , elementMetadata = NULL
>    , metadata = list()
> )
>    , ranges = new("IRanges"
>    , start = c(713844L, 762136L, 780124L, 780533L, 781104L, 793830L)
>    , width = c(644L, 1064L, 166L, 145L, 284L, 567L)
>    , NAMES = NULL
>    , elementType = "integer"
>    , elementMetadata = NULL
>    , metadata = list()
> )
>    , strand = new("Rle"
>    , values = structure(3L, .Label = c("+", "-", "*"), class = "factor")
>    , lengths = 6L
>    , elementMetadata = NULL
>    , metadata = list()
> )
>    , elementMetadata = new("DataFrame"
>    , rownames = NULL
>    , nrows = 6L
>    , listData = structure(list(edensity = c(1000L, 1000L, 519L, 516L,
> 601L, 610L
> ), epeak = c(256L, 771L, 74L, 68L, 140L, 290L), over = c(1L,
> 2L, 0L, 0L, 0L, 0L)), .Names = c("edensity", "epeak", "over"))
>    , elementType = "ANY"
>    , elementMetadata = NULL
>    , metadata = list()
> )
>    , seqinfo = new("Seqinfo"
>    , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14",
> "chr15",
> "chr16", "chr17", "chr18", "chr19", "chr2", "chr20", "chr21",
> "chr22", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9",
> "chrX", "chrY")
>    , seqlengths = c(NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_, NA_integer_,
> NA_integer_, NA_integer_, NA_integer_, NA_integer_)
>    , is_circular = c(NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
> NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA)
>    , genome = c(NA_character_, NA_character_, NA_character_,
> NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_,
> NA_character_, NA_character_, NA_character_, NA_character_, NA_character_
> )
> )
>    , metadata = list()
> )
> 
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> 
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