Dear All,

I am trying to figure out how to use the masked BSgenome object - I want to enable ALL masks.

Following help for "bsapply" I tried:

library(BSgenome.Hsapiens.UCSC.hg19.masked)
hg19 <- BSgenome.Hsapiens.UCSC.hg19.masked
param <- new("BSParams", X = hg19)
param@maskList <- c(AGAPS = TRUE, AMB = TRUE, RM = TRUE, TRF = TRUE)
bsapply(param)

Just to get:

Error in BSParams@FUN(seq, ...) : unused argument (seq)

I have tried many, many other combinations but none seem to work. I'd greatly appreciate any ideas on how to make it work.

Best regards,

Lukasz

PS:

active(masks(hg19$chr1))["RM"] <- TRUE

Error in `$<-`(`*tmp*`, "chr1", value = <S4 object of class "MaskedDNAString">) :
  no method for assigning subsets of this S4 class

but

c1 <- hg19$chr1

active(masks(c1))["RM"] <- TRUE

works ok! The problem is I need a whole genome, not split into chromosomes...

> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99 BSgenome.Hsapiens.UCSC.hg19_1.4.0         BSgenome_1.38.0                          
 [4] rtracklayer_1.30.1                        Biostrings_2.38.0                         XVector_0.10.0                           
 [7] GenomicRanges_1.22.1                      GenomeInfoDb_1.6.1                        IRanges_2.4.1                            
[10] S4Vectors_0.8.1                           BiocGenerics_0.16.1                      

loaded via a namespace (and not attached):
 [1] XML_3.98-1.3               Rsamtools_1.22.0           GenomicAlignments_1.6.1    bitops_1.0-6               futile.options_1.0.0      
 [6] zlibbioc_1.16.0            futile.logger_1.4.1        lambda.r_1.1.7             BiocParallel_1.4.0         tools_3.2.2               
[11] Biobase_2.30.0             RCurl_1.95-4.7             SummarizedExperiment_1.0.1