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

[Ivan Gregoretti]

Hi Everybody,

How do you resize 'width' according to strandedness?

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