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