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 <[email protected]> wrote: > Hi, > > On Thu, Apr 22, 2010 at 4:17 PM, Ivan Gregoretti <[email protected]> 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 > _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
