Hello,

I recognised a strange behaviour of range (gr). Shouldnt it treat the whole
grange object? Like ranges(gr)? But it doesnt.

What's wrong?
Thanks
Hermann

> gr
GRanges with 4 ranges and 1 metadata column:
             seqnames         ranges strand |       score
                <Rle>      <IRanges>  <Rle> | <character>
  rs55998931     chr1 [10492, 10492]      * |    0.115787
  rs58108140     chr1 [10583, 10583]      * |    0.394721
  rs75454623     chr1 [14930, 14930]      * |        0.48
  rs12401368     chr1 [66507, 66507]      * |    0.499191
  ---
  seqlengths:
              chr1           chr10 ...            chrX            chrY
                NA              NA ...              NA              NA
> ranges (gr)
IRanges of length 4
    start   end width      names
[1] 10492 10492     1 rs55998931
[2] 10583 10583     1 rs58108140
[3] 14930 14930     1 rs75454623
[4] 66507 66507     1 rs12401368
> range (gr)                # Only gives back gr[1]
GRanges with 1 range and 0 metadata columns:
      seqnames         ranges strand
         <Rle>      <IRanges>  <Rle>
  [1]     chr1 [10492, 66507]      *
  ---
  seqlengths:
              chr1           chr10 ...            chrX            chrY
                NA              NA ...              NA              NA
> dput (gr)
new("GRanges"
    , seqnames = new("Rle"
    , values = structure(1L, .Label = c("chr1", "chr10", "chr11", "chr12",
"chr13",
"chr14", "chr15", "chr16", "chr17", "chr17_ctg5_hap1", "chr18",
"chr19", "chr2", "chr20", "chr21", "chr22", "chr3", "chr4",
"chr4_ctg9_hap1",
"chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3",
"chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7",
"chr7", "chr8", "chr9", "chrM", "chrX", "chrY"), class = "factor")
    , lengths = 4L
    , elementMetadata = NULL
    , metadata = list()
)
    , ranges = new("IRanges"
    , start = c(10492L, 10583L, 14930L, 66507L)
    , width = c(1L, 1L, 1L, 1L)
    , NAMES = c("rs55998931", "rs58108140", "rs75454623", "rs12401368")
    , elementType = "integer"
    , elementMetadata = NULL
    , metadata = list()
)
    , strand = new("Rle"
    , values = structure(3L, .Label = c("+", "-", "*"), class = "factor")
    , lengths = 4L
    , elementMetadata = NULL
    , metadata = list()
)
    , elementMetadata = new("DataFrame"
    , rownames = NULL
    , nrows = 4L
    , listData = structure(list(score = c("0.115787", "0.394721", "0.48",
"0.499191"
)), .Names = "score")
    , elementType = "ANY"
    , elementMetadata = NULL
    , metadata = list()
)
    , seqinfo = new("Seqinfo"
    , seqnames = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14",
"chr15",
"chr16", "chr17", "chr17_ctg5_hap1", "chr18", "chr19", "chr2",
"chr20", "chr21", "chr22", "chr3", "chr4", "chr4_ctg9_hap1",
"chr5", "chr6", "chr6_apd_hap1", "chr6_cox_hap2", "chr6_dbb_hap3",
"chr6_mann_hap4", "chr6_mcf_hap5", "chr6_qbl_hap6", "chr6_ssto_hap7",
"chr7", "chr8", "chr9", "chrM", "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_, 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, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA)
    , genome = c("hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19",
"hg19",
"hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19",
"hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19",
"hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19", "hg19",
"hg19", "hg19")
)
    , metadata = list(<S4 object of class structure("DataFrame", package =
"IRanges")>)
)
> SessionInfo()
Fehler: konnte Funktion "SessionInfo" nicht finden
> sessionInfo()
R version 2.15.3 (2013-03-01)
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=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GenABEL_1.7-4        MASS_7.3-23          GenomicRanges_1.10.7
[4] IRanges_1.16.6       BiocGenerics_0.4.0

loaded via a namespace (and not attached):
[1] compiler_2.15.3 parallel_2.15.3 stats4_2.15.3   tools_2.15.3

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