maskedBSgenome - cannot enable masks
0
0
Entering edit mode
kielpinski • 0
@kielpinski-8492
Last seen 9.0 years ago
Denmark

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

 

 

mask bsgenome • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 910 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6