Question: bsseq - error with dmrFinder
0
gravatar for varunorama
23 months ago by
varunorama0
University of Kentucky
varunorama0 wrote:

Hello,

I am having some trouble with the dmrFinder function that is part of bsseq. The code that I running

>BS.cov = getCoverage(rrbs.smoothed)
>keepLoci.ex = which(rowSums(BS.cov[,rrbs$Type == "Control"] > 0) >= 10 &
                      rowSums(BS.cov[,rrbs$Type == "Regen"] > 0) >= 9 )

>rrbs.smoothed2 = rrbs.smoothed[keepLoci.ex,]

>rrbs.fitted.tstat = BSmooth.tstat(rrbs.smoothed2, 
                                  group1 = c("Day0-C","6Hr-C","12Hr-C","24Hr-C","48Hr-C",
                                             "72Hr-C","96Hr-C","120Hr-C","144Hr-C","168Hr-C"),
                                  group2 = c("6Hr-T","12Hr-T","24Hr-T","48Hr-T",
                                             "72Hr-T","96Hr-T","120Hr-T","144Hr-T","168Hr-T"),
                                  estimate.var = "group2",
                                  local.correct = TRUE,
                                  verbose=TRUE)

>dmrs0 = dmrFinder(rrbs.fitted.tstat)

receives an error:

Error in quantile.default(x, ...) : 
  missing values and NaN's not allowed if 'na.rm' is FALSE

I take it that the reason for this error is because there are missing values in the rrbs.fitted.tstat object.

Is there a way to disregard these missing values when considering the rrbs.fitted.tstat class? I've tried na.omit(rrbs.fitted.tstat) but that did not work.

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] bsseq_1.12.2               SummarizedExperiment_1.6.3 DelayedArray_0.2.7         matrixStats_0.52.2         Biobase_2.36.2            
 [6] GenomicRanges_1.28.4       GenomeInfoDb_1.12.2        IRanges_2.10.2             S4Vectors_0.14.3           BiocGenerics_0.22.0       
[11] BiocInstaller_1.26.0      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12            XVector_0.16.0          zlibbioc_1.22.0         munsell_0.4.3           colorspace_1.3-2       
 [6] lattice_0.20-35         plyr_1.8.4              tools_3.4.1             grid_3.4.1              data.table_1.10.4      
[11] R.oo_1.21.0             gtools_3.5.0            permute_0.9-4           Matrix_1.2-10           GenomeInfoDbData_0.99.0
[16] R.utils_2.5.0           bitops_1.0-6            RCurl_1.95-4.8          limma_3.32.5            compiler_3.4.1         
[21] R.methodsS3_1.7.1       scales_0.5.0            locfit_1.5-9.1    

 

bsseq r package dmrfinder • 398 views
ADD COMMENTlink written 23 months ago by varunorama0
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