Entering edit mode
9.7 years ago
Aishwarya.Kulkarni
▴
30
I am using Biostrings package matchPWM method and I am using the following steps:
> library(BSgenome.Hsapiens.UCSC.hg19)
> #loading my pwm
>matchPWM(pwm, Hsapiens)
Error in .normargSubject(subject) :
active masks are not supported yet, please complain!
What is the error about and what can be done to overcome it?
Also here are the session specifications:
> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.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=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BSgenome.Hsapiens.UCSC.hg19_1.3.19 BSgenome_1.26.1
[3] GenomicRanges_1.10.7 Biostrings_2.26.3
[5] IRanges_1.16.6 BiocGenerics_0.4.0
loaded via a namespace (and not attached):
[1] parallel_2.15.3 stats4_2.15.3 tools_2.15.3
I did try to use the command and it threw me an error:
Well, when you iterate over a BSgenome, you end up processing the chromosomes, which are DNAStrings. They actually shouldn't be MaskedDNAStrings, so it's a bit odd that you're running into this. You might post a reproducible example (just an example PWM that causes this) or just post to the Bioconductor email list so the package authors can have a look.