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

[Ivan Gregoretti]

Cool. I'll try it. Thank you.

Ivan

Ivan Gregoretti, PhD
National Institute of Diabetes and Digestive and Kidney Diseases
National Institutes of Health




On Thu, Apr 22, 2010 at 5:11 PM, Steve Lianoglou
<mailinglist.honeypot at gmail.com> wrote:
> Hi,
>
> On Thu, Apr 22, 2010 at 4:17 PM, Ivan Gregoretti <ivangreg at gmail.com> wrote:
>> Hello everybody,
>>
>> How do you resize() the ranges of a RangedData object?
>>
>>
>> In the past (IRanges 1.4.11), I could
>>
>> 1) extend forward 200 bases from the start in '+' ranges OR
>> 2) extend backward 200 bases from the end in '-' ranges.
>>
>> The syntax was something like this:
>>
>> resize(ranges(A), width = 200, start = A$strand == "+")
>>
>> In IRanges 1.5.70, the "start" argument of resize() has been
>> depracated and replaced by "fix".
>>
>> Can somebody show how to get the task accomplished with the new resize()?
>
> I'm pretty sure you use `fix` just like you use start:
>
> R> strands <- c("+", '-', '+', '-', '-')
> R> ir <- IRanges(c(1,10,20,30, 40), width=5)
> R> ir
> IRanges of length 5
>    start end width
> [1]     1   5     5
> [2]    10  14     5
> [3]    20  24     5
> [4]    30  34     5
> [5]    40  44     5
>
> R> resize(ir, width=8, fix=ifelse(strands == '+', 'start', 'end'))
> IRanges of length 5
>    start end width
> [1]     1   8     8
> [2]     7  14     8
> [3]    20  27     8
> [4]    27  34     8
> [5]    37  44     8
>
> --
> Steve Lianoglou
> Graduate Student: Computational Systems Biology
>  | Memorial Sloan-Kettering Cancer Center
>  | Weill Medical College of Cornell University
> Contact Info: http://cbio.mskcc.org/~lianos/contact
>