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

[Patrick Aboyoun]

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). 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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