[BioC] genome_intervals and GRange objects/HiTC package

[Valerie Obenchain]

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]]
>
> _______________________________________________
> 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