[BioC] can not coerce CompressedIntegerList to vector or integer in 'IRanges' package

[Patrick Aboyoun]

Since it was easy to do and you guys find it useful, I just added 
as.logical, as.integer, as.numeric., as.complex, as.character, as.raw, 
and as.factor methods for AtomicList objects to BioC 2.5. Thus you can 
take any AtomicList type (e.g. CompressedIntegerList) and convert it to 
an atomic vector type by using the appropriate as.* function. This 
change will be available from bioconductor.org (via biocLite) tomorrow 
afternoon PDT or at hedgehog.fhcrc.org (via svn) immediately.


Cheers,
Patrick


Michael Lawrence wrote:
>
>
> On Tue, Sep 22, 2009 at 7:35 AM, Patrick Aboyoun <paboyoun at fhcrc.org 
> <mailto:paboyoun at fhcrc.org>> wrote:
>
>     LiGang,
>     The unlist command will get you what you are looking for.
>     AtomicList objects should be thought of as typed lists (as.integer
>     on a regular list containing integer elements will also throw an
>     error). 
>
>
> Calling as.integer() works on a list where all the elements are of 
> length one, like with sapply(). This has always been surprising to me. 
> Why would it work in one case, but not in general? The list structure 
> is implicitly removed in both. The question is, if IRanges supported 
> as.integer/vector etc on atomic Lists, would this be more or less 
> surprising to the user? To me and apparently Li Gang as well, 
> as.integer() sounds like "make this an atomic integer vector", and 
> there is one obvious way to do that. Would introducing an 
> inconsistency with the base R list be so bad in this case?
>
> Michael
>  
>
>     Using your example I get:
>
>     <<Full code given below>>
>     > inter
>     CompressedIntegerList: 2 elements
>     names(2): chr1 chr2
>     > unlist(inter)
>     chr1 chr1 chr1 chr2 chr2 chr2 chr2
>      1    2    3   15   45   20    1
>     > unlist(inter, use.names=FALSE)
>     [1]  1  2  3 15 45 20  1
>     > sessionInfo()
>     R version 2.10.0 Under development (unstable) (2009-09-21 r49771)
>     i386-apple-darwin9.8.0
>
>     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_1.3.78
>
>
>     loaded via a namespace (and not attached):
>     [1] tools_2.10.0
>
>
>
>     Patrick
>
>
>
>     LiGang wrote:
>
>         can not coerce "CompressedIntegerList" to vector or integer
>
>
>         #====================================
>         ranges <- IRanges(c(1,2,3),c(4,5,6))
>         filter <- c(1L, 0L, 1L)
>         score <- c(10L, 2L, NA)
>         range2 <- IRanges(start=c(15,45,20,1), end=c(15,100,80,5))
>         both <- c(ranges, range2)
>         score <- c(score, c(0L, 3L, NA, 22L))
>         filter <- c(filter, c(0L, 1L, NA, 0L)) chrom <- paste("chr",
>         rep(c(1,2), c(length(ranges), length(range2))), sep="")
>         rd <- RangedData(both, score, filter, space = chrom, universe
>         = "hg18")
>
>         start(ranges(rd))->inter
>         as.vector(inter)
>
>         #Error in as.vector(inter) : # no method for coercing this S4
>         class to a vector
>
>         as.integer(inter)
>
>         #Error in as.integer(inter) : #  cannot coerce type 'S4' to
>         vector of type 'integer'
>         #====================================
>          sessionInfo()
>         R version 2.10.0 Under development (unstable) (2009-09-14
>         r49685) i386-pc-mingw32
>         locale:
>         [1] LC_COLLATE=English_United States.1252
>          LC_CTYPE=English_United States.1252  
>          LC_MONETARY=English_United States.1252
>         [4] LC_NUMERIC=C                          
>         LC_TIME=English_United States.1252    
>         attached base packages:
>         [1] grid      stats     graphics  grDevices utils     datasets
>          methods   base    
>         other attached packages:
>         [1] rtracklayer_1.5.14 RCurl_1.2-0        bitops_1.0-4.1    
>         Rgraphviz_1.23.4   graph_1.23.4       IRanges_1.3.77    
>         loaded via a namespace (and not attached):
>         [1] Biobase_2.5.6      Biostrings_2.13.40 BSgenome_1.13.12  
>         Rcompression_0.6-
>         0 tools_2.10.0       XML_2.6-0  
>
>
>
>         ---
>         LiGang
>
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