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

[Steve Lianoglou]

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