bsseq - dmrFinder error
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parker • 0
@parker-7456
Last seen 4.4 years ago
Switzerland

Hello,

I have previously used the bsseq package to get a list of dmrs successfully. However, now I have encountered an error when I run the dmrFinder - please see below:

Any help is much appreciated.

Thank you!

Hannah

> data.tstat

An object of type 'BSseqTstat' with
  3142216 methylation loci
based on smoothed data:
  BSmooth (ns = 20, h = 500, maxGap = 100000000)
with parameters
  BSmooth.tstat (local.correct = TRUE, maxGap = 100000000)

> dmrs_quantil <- dmrFinder(data.tstat, qcutoff=c(0.005,0.995))
Error in (1 - h) * qs[i] : non-numeric argument to binary operator

 

R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

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

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

other attached packages:
[1] bsseq_1.10.0               limma_3.30.13             
[3] SummarizedExperiment_1.4.0 Biobase_2.34.0            
[5] GenomicRanges_1.26.2       GenomeInfoDb_1.10.3       
[7] IRanges_2.8.2              S4Vectors_0.12.1          
[9] BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.11       XVector_0.14.1     zlibbioc_1.20.0    munsell_0.4.3     
 [5] colorspace_1.3-2   lattice_0.20-35    plyr_1.8.4         grid_3.3.1        
 [9] data.table_1.10.4  R.oo_1.21.0        gtools_3.5.0       matrixStats_0.52.2
[13] permute_0.9-4      Matrix_1.2-8       R.utils_2.5.0      bitops_1.0-6      
[17] RCurl_1.95-4.8     R.methodsS3_1.7.1  scales_0.4.1       locfit_1.5-9.1 

bsseq r package bsmooth dmrFinder • 760 views
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