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

[Ivan Gregoretti]

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
>
>