[BioC] error when coercing GenomeData to RangedData: 'no method or default for coercing “XStringViews” to “RangedData”'

[Ludo Pagie]

Hi all,

I'm getting an error when trying to coerce a GenomeData object to a
RangedData object. Here's the code I have used together with some
output (in particular the error msg when coercing):


######################################################################
# import human genome sequence
library(BSgenome.Hsapiens.UCSC.hg19)

# Virtual digest of the entire genome in GATC fragments:
# matchPattern to find GATC motifs, using bsapply
ExtractGATCFragments <- function(chr) {
# function for finding GATC sites in a chromosome and returning the fragments
  # starting and ending with GATC
  GATC.match <- matchPattern(chr, pattern='GATC')
  start <- c(1, start(GATC.match)) # not sure what happens if
chromosome starts with GATC
  end <- c(end(GATC.match), length(chr))
  Views(subject=unmasked(chr),start=start, end=end)
}
pm <- new('BSParams', X=Hsapiens, FUN=function(chr) ExtractGATCFragments(chr) )
# create the GenomeData object:
GATC.fragments <- bsapply(pm)

# is it a genomeData??
class(GATC.fragments)
# [1] "GenomeData"
# attr(,"package")
# [1] "BSgenome"

# coerce it to a RangedData:
as(GATC.fragments, "RangedData")
# Error in FUN(X[[1L]], ...) :
#   no method or default for coercing “XStringViews” to “RangedData”



> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.30.0
[3] Biostrings_2.30.1                  GenomicRanges_1.14.4
[5] XVector_0.2.0                      IRanges_1.20.6
[7] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
[1] stats4_3.0.2 tools_3.0.2
######################################################################

Can anybody point out to me why the object can not be coerced.

Thanks, Ludo