Entering edit mode
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