Dear Valerie,
thanks for answering.

This is my session:

> library (HiTC)
Lade nötiges Paket: girafe
Lade nötiges Paket: IRanges
Lade nötiges Paket: BiocGenerics

Attache Paket: ‘BiocGenerics’

The following object(s) are masked from ‘package:stats’:

    xtabs

The following object(s) are masked from ‘package:base’:

    anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
    get, intersect, lapply, Map, mapply, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rbind, Reduce, rep.int,
    rownames, sapply, setdiff, table, tapply, union, unique

Lade nötiges Paket: Rsamtools
Lade nötiges Paket: GenomicRanges
Lade nötiges Paket: Biostrings
Lade nötiges Paket: ShortRead
Lade nötiges Paket: lattice
Lade nötiges Paket: latticeExtra
Lade nötiges Paket: RColorBrewer
Lade nötiges Paket: intervals

Attache Paket: ‘intervals’

The following object(s) are masked from ‘package:Biostrings’:

    type

The following object(s) are masked from ‘package:GenomicRanges’:

    reduce

The following object(s) are masked from ‘package:IRanges’:

    expand, reduce

Lade nötiges Paket: genomeIntervals
Lade nötiges Paket: grid
Warnmeldungen:
1: vorhergehender Import ‘coerce’ während des Ladens von ‘intervals’
ersetzt
2: vorhergehender Import ‘initialize’ während des Ladens von ‘intervals’
ersetzt
> exDir <- system.file("extdata", package="HiTC")
> hC <-
import.my5C(file.path(exDir,"HIC_gm06690_chr14_chr14_1000000_obs.txt"))
Convert my5C matrix file in HiTC object(s)
Loading chr14-chr14...
> detail (hC$chr14chr14)
HTC object
Focus on genomic region [chr14:1-106368584]
Matrix of Interaction data: [107-107]
107  genome intervals from 'xgi' object
107  genome intervals from 'ygi' object
Total Reads = 755139
Number of Interactions =  7913
Median Frequency =  30
> hC.gr <- y_intervals (hC$chr14chr14)
> hC.gr
Object of class Genome_intervals
107 base intervals and 0 inter-base intervals(*):
chr14 [1, 999999]
chr14 [1e+06, 1999999]
chr14 [2e+06, 2999999]
chr14 [3e+06, 3999999]
... 99 other intervals...
chr14 [1.03e+08, 103999999]
chr14 [1.04e+08, 104999999]
chr14 [1.05e+08, 105999999]
chr14 [1.06e+08, 106368584]

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
... 99 other intervals...
    seq_name         id inter_base
104    chr14 HIC_bin104      FALSE
105    chr14 HIC_bin105      FALSE
106    chr14 HIC_bin106      FALSE
107    chr14 HIC_bin107      FALSE
> hC.subset <- hC.gr[1:5,]
> dput(hC.subset)
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"
)
> sessionInfo()
R version 2.15.2 (2012-10-26)
Platform: i686-pc-linux-gnu (32-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] grid      stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
 [1] HiTC_1.2.0             girafe_1.10.0          genomeIntervals_1.14.0
 [4] intervals_0.13.3       ShortRead_1.16.3       latticeExtra_0.6-24
 [7] RColorBrewer_1.0-5     lattice_0.20-13        Rsamtools_1.10.2
[10] Biostrings_2.26.3      GenomicRanges_1.10.6   IRanges_1.16.4
[13] BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] Biobase_2.18.0   bitops_1.0-5     BSgenome_1.26.1  colorspace_1.2-1
 [5] compiler_2.15.2  dichromat_2.0-0  digest_0.6.2     ggplot2_0.9.3
 [9] gtable_0.1.2     hwriter_1.3      labeling_0.1     MASS_7.3-23
[13] munsell_0.4      parallel_2.15.2  plyr_1.8         proto_0.3-10
[17] reshape2_1.2.2   scales_0.2.3     stats4_2.15.2    stringr_0.6.2
[21] tools_2.15.2     zlibbioc_1.4.0
>

2013/2/6 Valerie Obenchain <vobencha@fhcrc.org>

> Hi Herman,
>
> When you post a question please provide code that reproduces the problem.
> Your example does not show how 'hic.gr' was created or what kind of
> object it is.
>
> library(HiTC)
> data(Nora_5C)
> intervals <- y_intervals(E14sub)
>
> The 'intervals' object is a GRanges.
>
> > class(intervals)
> [1] "GRanges"
> attr(,"package")
> [1] "GenomicRanges"
>
> You can extract metadata colums with 'mcols'.
>
> head(mcols(intervals))
>
> > head(mcols(intervals))
> DataFrame with 6 rows and 4 columns
>          name     score     itemRgb                thick
>   <character> <numeric> <character>            <IRanges>
> 1       FOR_3         0     #0000FF [98834146, 98837506]
> 2       FOR_5         0     #0000FF [98840772, 98841227]
> 3       FOR_7         0     #0000FF [98843249, 98848364]
> 4       FOR_9         0     #0000FF [98849664, 98850577]
> 5      FOR_13         0     #0000FF [98862022, 98867230]
> 6      FOR_15         0     #0000FF [98869143, 98870524]
>
> Also use 'mcols' to set the value of a metadata column.
>
> intervals$newData <- seq_along(intervals)
> > head(mcols(intervals))
> DataFrame with 6 rows and 5 columns
>          name     score     itemRgb                thick   newData
>   <character> <numeric> <character>            <IRanges> <integer>
> 1       FOR_3         0     #0000FF [98834146, 98837506]         1
> 2       FOR_5         0     #0000FF [98840772, 98841227]         2
> 3       FOR_7         0     #0000FF [98843249, 98848364]         3
> 4       FOR_9         0     #0000FF [98849664, 98850577]         4
> 5      FOR_13         0     #0000FF [98862022, 98867230]         5
> 6      FOR_15         0     #0000FF [98869143, 98870524]         6
>
>
> It looks like y_intervals() is returning a valid GRanges. Can you provide
> an example of how you are getting a 'Genome_interval' object?
>
> Valerie
>
>
>
>
> On 02/05/2013 01:05 PM, Hermann Norpois wrote:
>
>> Hello,
>>
>> in the documentation of HiTC package y_intervals () is described as a
>> method to "return the ygi GRanges object defining the y intervals". I
>> tried
>> this for the test data (see dput) and expected a "classical" GRange
>> object.
>> For instance I would like to do an operation like
>>
>> mcols (hic.gr)$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"
>> )
>>
>>         [[alternative HTML version deleted]]
>>
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>
>

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