[BioC] IRanges: the width argument of the coverage function

[Nicolas Delhomme]

Hi,

I thought I saw a mention on the mailing list that coverage and similar functions would support a named vector for providing the width instead of just a list. The documentation states so too:

For RangesList and RangedData objects, a list or vector of
          the same length as ‘x’ to be used for the corresponding
          element in ‘x’.

However, using a named vector does not work (my aln.ranges is a RangesList object):

> class(aln.ranges)
[1] "CompressedIRangesList"
attr(,"package")
[1] "IRanges"

> coverage(aln.ranges,width=chrSize(obj))
Error in .local(x, shift, width, weight, ...) : 
  'width' must be a non-empty list

> str(chrSize(obj)) # that's my width
 Named int [1:2518] 48367220 21538349 8012 10863 7999 7999 7991 8236 7962 8324 ...
 - attr(*, "names")= chr [1:2518] "scaffold_1" "scaffold_10" "scaffold_1000" "scaffold_1001" ...

Changing the width to a list works:
> coverage(aln.ranges,width=as.list(chrSize(obj)))

So, I'm just curious what the status is. 

Thanks,

Nico

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] easyRNASeq_1.3.6       ShortRead_1.15.9       latticeExtra_0.6-19   
 [4] RColorBrewer_1.0-5     lattice_0.20-6         Rsamtools_1.9.18      
 [7] DESeq_1.9.7            locfit_1.5-8           BSgenome_1.25.3       
[10] GenomicRanges_1.9.28   Biostrings_2.25.6      edgeR_2.7.24          
[13] limma_3.13.7           biomaRt_2.13.1         Biobase_2.17.6        
[16] genomeIntervals_1.13.2 intervals_0.13.3       IRanges_1.15.17       
[19] BiocGenerics_0.3.0    

loaded via a namespace (and not attached):
 [1] annotate_1.35.3       AnnotationDbi_1.19.15 bitops_1.0-4.1       
 [4] DBI_0.2-5             genefilter_1.39.0     geneplotter_1.35.0   
 [7] grid_2.15.1           hwriter_1.3           RCurl_1.91-1         
[10] RSQLite_0.11.1        splines_2.15.1        stats4_2.15.1        
[13] survival_2.36-14      tools_2.15.1          XML_3.9-4            
[16] xtable_1.7-0          zlibbioc_1.3.0       


---------------------------------------------------------------
Nicolas Delhomme

Genome Biology Computational Support

European Molecular Biology Laboratory

Tel: +49 6221 387 8310
Email: nicolas.delhomme at embl.de
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany