[Bioc-sig-seq] RangedData objects. Redefining widths with conditions.

[Ivan Gregoretti]

I got it. It should read

resize(ranges(A), width = 1, start = A$strand == "+")

Thank you!

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health
5 Memorial Dr, Building 5, Room 205.
Bethesda, MD 20892. USA.
Phone: 1-301-496-1592
Fax: 1-301-496-9878



On Tue, Feb 16, 2010 at 2:27 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
> Apparently resize() does not like my RangedData:
>
>> A
> RangedData with 5 rows and 1 value column across 2 spaces
>            space       ranges |      strand
>      <character>    <IRanges> | <character>
> gene1        chr1 [1001, 1500] |           +
> gene2        chr1 [3501, 4000] |           -
> gene3        chr1 [7001, 8500] |           +
> gene4        chr2 [ 601, 1300] |           -
> gene5        chr2 [2201, 2300] |           +
>
>> resize(ranges(A), start = A$strand == "+")
> Error in resize(x at unlistData, width = width, start = start, use.names
> = use.names) :
>  element 1 is empty;
>   the part of the args list of 'is.numeric' being evaluated was:
>   (width)
>
> Am I missing something?
>
> Thank you.
>
> Ivan
>
>
> Ivan Gregoretti, PhD
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> 5 Memorial Dr, Building 5, Room 205.
> Bethesda, MD 20892. USA.
> Phone: 1-301-496-1592
> Fax: 1-301-496-9878
>
>
>
> On Tue, Feb 16, 2010 at 1:38 PM, Michael Lawrence
> <lawrence.michael at gene.com> wrote:
>>
>>
>> On Tue, Feb 16, 2010 at 10:26 AM, Ivan Gregoretti <ivangreg at gmail.com>
>> wrote:
>>>
>>> Hi Everybody,
>>>
>>> How do you resize 'width' according to strandedness?
>>>
>>
>> Something like:
>>
>> ranges(rd) <- resize(ranges(rd), start = rd$stand == "+")
>>
>>>
>>> For example, lets say I have
>>>
>>> A <- RangedData(IRanges(start=c(1001, 3501, 7001, 601, 2201),
>>>                        end=c(1500, 4000, 8500, 1300, 2300),
>>>                        names=c("gene1", "gene2", "gene3", "gene4",
>>> "gene5")),
>>>                space=c("chr1", "chr1", "chr1", "chr2", "chr2"),
>>>                strand=c("+", "-", "+", "-", "+"))
>>>
>>> > A
>>> RangedData with 5 rows and 1 value column across 2 spaces
>>>            space       ranges |      strand
>>>      <character>    <IRanges> | <character>
>>> gene1        chr1 [1001, 1500] |           +
>>> gene2        chr1 [3501, 4000] |           -
>>> gene3        chr1 [7001, 8500] |           +
>>> gene4        chr2 [ 601, 1300] |           -
>>> gene5        chr2 [2201, 2300] |           +
>>>
>>> Now I want to resize the widths to a single nucleotide starting at
>>> 'start' when the strand is '+' or starting at
>>> 'end' if the strand is '-'.
>>> The end product should be this:
>>>
>>> B <- RangedData(IRanges(start=c(1001, 4000, 7001, 1300, 2101),
>>>                        end=c(1001, 4000, 7001, 1300, 2201),
>>>                        names=c("gene1", "gene2", "gene3", "gene4",
>>> "gene5")),
>>>                space=c("chr1", "chr1", "chr1", "chr2", "chr2"),
>>>                strand=c("+", "-", "+", "-", "+"))
>>> > B
>>>
>>> RangedData with 5 rows and 1 value column across 2 spaces
>>>            space       ranges |      strand
>>>      <character>    <IRanges> | <character>
>>> gene1        chr1 [1001, 1001] |           +
>>> gene2        chr1 [4000, 4000] |           -
>>> gene3        chr1 [7001, 7001] |           +
>>> gene4        chr2 [1300, 1300] |           -
>>> gene5        chr2 [2101, 2201] |           +
>>>
>>> I wonder if there is a concise way of achieving this manipulation.
>>>
>>> For a wordy version, you can always count on me. :)
>>>
>>> Thank you,
>>>
>>> Ivan
>>>
>>> > sessionInfo()
>>> R version 2.10.0 (2009-10-26)
>>> x86_64-redhat-linux-gnu
>>>
>>> locale:
>>>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>> LC_TIME=en_US.UTF-8
>>>  [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=C
>>> LC_MESSAGES=en_US.UTF-8
>>>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>> LC_ADDRESS=C
>>> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8
>>> LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] grid      splines   stats     graphics  grDevices utils
>>> datasets  methods
>>> [9] base
>>>
>>> other attached packages:
>>>  [1] org.Mm.eg.db_2.3.6                  ChIPpeakAnno_1.2.3
>>>  [3] org.Hs.eg.db_2.3.6                  GO.db_2.3.5
>>>  [5] RSQLite_0.8-2                       AnnotationDbi_1.8.1
>>>  [7] BSgenome.Ecoli.NCBI.20080805_1.3.16 BSgenome_1.14.2
>>>  [9] multtest_2.2.0                      Biobase_2.6.1
>>> [11] biomaRt_2.2.0                       RMySQL_0.7-4
>>> [13] DBI_0.2-5                           gplots_2.7.4
>>> [15] caTools_1.10                        gdata_2.7.1
>>> [17] gtools_2.6.1                        lattice_0.18-3
>>> [19] Hmisc_3.7-0                         survival_2.35-8
>>> [21] Biostrings_2.14.12                  IRanges_1.4.11
>>> [23] rtracklayer_1.6.0                   RCurl_1.3-1
>>> [25] bitops_1.0-4.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] cluster_1.12.1 MASS_7.3-3     tools_2.10.0   XML_2.6-0
>>>
>>>
>>> Ivan Gregoretti, PhD
>>> National Institute of Diabetes and Digestive and Kidney Diseases
>>> National Institutes of Health
>>> 5 Memorial Dr, Building 5, Room 205.
>>> Bethesda, MD 20892. USA.
>>> Phone: 1-301-496-1592
>>> Fax: 1-301-496-9878
>>>
>>> _______________________________________________
>>> Bioc-sig-sequencing mailing list
>>> Bioc-sig-sequencing at r-project.org
>>> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
>>
>>
>