Hello,

in the documentation of HiTC package y_intervals () is described as a
method to "return the ygi GRanges object defining the y intervals". I tried
this for the test data (see dput) and expected a "classical" GRange object.
For instance I would like to do an operation like

mcols (hic.gr)$test <- 1

But it did not work as hic.gr is a Genome_interval object (as dput
mentioned). Can I transform this in a classical GR-object allowing
mcols-operations? Can anybody comment on the difference between
Genome_interval an Grange?


Thanks
Hermann



> hic.gr
Object of class Genome_intervals
5 base intervals and 0 inter-base intervals(*):
chr14 [1, 999999]
chr14 [1e+06, 1999999]
chr14 [2e+06, 2999999]
chr14 [3e+06, 3999999]
chr14 [4e+06, 4999999]

annotation:
  seq_name       id inter_base
1    chr14 HIC_bin1      FALSE
2    chr14 HIC_bin2      FALSE
3    chr14 HIC_bin3      FALSE
4    chr14 HIC_bin4      FALSE
5    chr14 HIC_bin5      FALSE

> dput (hic.gr)
new("Genome_intervals"
    , .Data = structure(c(1, 1e+06, 2e+06, 3e+06, 4e+06, 999999, 1999999,
2999999,
3999999, 4999999), .Dim = c(5L, 2L))
    , annotation = structure(list(seq_name = structure(c(1L, 1L, 1L, 1L,
1L), .Label = "chr14", class = "factor"),
    id = structure(c(1L, 20L, 31L, 42L, 53L), .Label = c("HIC_bin1",
    "HIC_bin10", "HIC_bin100", "HIC_bin101", "HIC_bin102", "HIC_bin103",
    "HIC_bin104", "HIC_bin105", "HIC_bin106", "HIC_bin107", "HIC_bin11",
    "HIC_bin12", "HIC_bin13", "HIC_bin14", "HIC_bin15", "HIC_bin16",
    "HIC_bin17", "HIC_bin18", "HIC_bin19", "HIC_bin2", "HIC_bin20",
    "HIC_bin21", "HIC_bin22", "HIC_bin23", "HIC_bin24", "HIC_bin25",
    "HIC_bin26", "HIC_bin27", "HIC_bin28", "HIC_bin29", "HIC_bin3",
    "HIC_bin30", "HIC_bin31", "HIC_bin32", "HIC_bin33", "HIC_bin34",
    "HIC_bin35", "HIC_bin36", "HIC_bin37", "HIC_bin38", "HIC_bin39",
    "HIC_bin4", "HIC_bin40", "HIC_bin41", "HIC_bin42", "HIC_bin43",
    "HIC_bin44", "HIC_bin45", "HIC_bin46", "HIC_bin47", "HIC_bin48",
    "HIC_bin49", "HIC_bin5", "HIC_bin50", "HIC_bin51", "HIC_bin52",
    "HIC_bin53", "HIC_bin54", "HIC_bin55", "HIC_bin56", "HIC_bin57",
    "HIC_bin58", "HIC_bin59", "HIC_bin6", "HIC_bin60", "HIC_bin61",
    "HIC_bin62", "HIC_bin63", "HIC_bin64", "HIC_bin65", "HIC_bin66",
    "HIC_bin67", "HIC_bin68", "HIC_bin69", "HIC_bin7", "HIC_bin70",
    "HIC_bin71", "HIC_bin72", "HIC_bin73", "HIC_bin74", "HIC_bin75",
    "HIC_bin76", "HIC_bin77", "HIC_bin78", "HIC_bin79", "HIC_bin8",
    "HIC_bin80", "HIC_bin81", "HIC_bin82", "HIC_bin83", "HIC_bin84",
    "HIC_bin85", "HIC_bin86", "HIC_bin87", "HIC_bin88", "HIC_bin89",
    "HIC_bin9", "HIC_bin90", "HIC_bin91", "HIC_bin92", "HIC_bin93",
    "HIC_bin94", "HIC_bin95", "HIC_bin96", "HIC_bin97", "HIC_bin98",
    "HIC_bin99"), class = "factor"), inter_base = c(FALSE, FALSE,
    FALSE, FALSE, FALSE)), .Names = c("seq_name", "id", "inter_base"
), row.names = c(NA, 5L), class = "data.frame")
    , closed = structure(c(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,
TRUE,
TRUE), .Dim = c(5L, 2L))
    , type = "Z"
)

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