[BioC] Repitools - featureScores - mappability Bsgenome object

[Jaritz,Markus]

Dear colleagues,
dear Mark,

Many thanks for providing the "Repitools "package, it is of great help.
There, the function "featureScores" allows for considering mappability for reads 
via a BSgenome object.

Is there any such "mappability-based" BSgenome available,
especially for Mus musculus? I could not find one
(not even the one mentioned in the Repitools vignette, 
"BSgenome.Hsapiens36bp.UCSC.hg18mappability_1.0").

In case there is none, I assume I need to forge
my own mappability masked version of the Mus musculus
genome (or several, for each read length), and provide this 
as a parameter to the featureScores function? Or is this 
an overkill and masking just the regions considered
in the analysis (e.g., peak regions) is sufficient?

Thank you for any hint!

Kind regards

Markus

Dr. Markus Jaritz
IMP - Research Institute of Molecular Pathology

sessionInof()


R version 2.15.2 (2012-10-26)
Platform: x86_64-pc-linux-gnu (64-bit)

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

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

other attached packages:
[1] BiocInstaller_1.8.3                Biobase_2.18.0                    
[3] Repitools_1.4.2                    BSgenome.Mmusculus.UCSC.mm9_1.3.19
[5] BSgenome_1.26.1                    Biostrings_2.26.3                 
[7] GenomicRanges_1.10.7               IRanges_1.16.6                    
[9] BiocGenerics_0.4.0                

loaded via a namespace (and not attached):
[1] edgeR_3.0.8     limma_3.14.4    parallel_2.15.2 stats4_2.15.2  
[5] tcltk_2.15.2    tools_2.15.2