[BioC] request: calculate coverage with weight on RangedData object

[Janet Young]

Hi,

I'm trying to calculate coverage using weights on a RangedData object  
(seems to work for simple IRanges objects, but not on RangedData).

I've found a workaround, but wanted to request an enhancement to be  
able to do this directly without the workaround. I think the code  
below should show you what I'm talking about.

thanks very much,

Janet Young

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Dr. Janet Young (Trask lab)

Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., C3-168,
P.O. Box 19024, Seattle, WA 98109-1024, USA.

tel: (206) 667 1471 fax: (206) 667 6524
email: jayoung  ...at...  fhcrc.org

http://www.fhcrc.org/labs/trask/

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library(IRanges)

### coverage with weights works for IRanges object
x <- IRanges(start=1:5,end=3:7)
coverage(x,weight=1:5)
### 'integer' Rle of length 7 with 7 runs
###   Lengths:  1  1  1  1  1  1  1
###   Values :  1  3  6  9 12  9  5

### but is not so well on RangedData
y <- RangedData(IRanges(start=c(1:5,1:5),end=c(3:7,3:7)),
                  space=c(rep("chrA",5),rep("chrB",5)),
                  score=c(1:5,1:5) )

coverage(y)  ## works, produces SimpleRleList

coverage(y,weight=y$score)  ## does not work
###  Error in weight[[i]] : subscript out of bounds

coverage(y,weight=rep(1,10))  ## does not work
###  Error in weight[[i]] : subscript out of bounds

### temporary workaround - iterate through spaces
mycov <- list()
for (thisspace in names(y)) {
     mycov[[thisspace]] <- coverage(ranges(y[thisspace]) 
[[1]],weight=y[thisspace]$score)
}
mycov
### $chrA
### 'integer' Rle of length 7 with 7 runs
###   Lengths:  1  1  1  1  1  1  1
###   Values :  1  3  6  9 12  9  5
###
### $chrB
### 'integer' Rle of length 7 with 7 runs
###   Lengths:  1  1  1  1  1  1  1
###   Values :  1  3  6  9 12  9  5

sessionInfo()

R version 2.10.1 (2009-12-14)
i386-apple-darwin8.11.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] IRanges_1.4.15