Hello, I am working with Bsseq to find DMRs in single replicate samples (Control and Expt) from WGBS. The bsseq object creation and smoothing worked well. Although, I encounter errors in the BSmooth.tstat function.
BS.OBJ.tstat = BSmooth.tstat(BS.OBJ.keep, group1="Control", group2="Expt", estimate.var = "paired", local.correct = TRUE, verbose = TRUE)
Error: length(group1) + length(group2) >= 3 is not TRUE
OR sometimes the error is
[BSmooth.tstat] preprocessing ... done in 2.5 sec
[BSmooth.tstat] computing stats within groups ... done in 0.4 sec
[BSmooth.tstat] computing stats across groups ... Error in approxfun(xx, yy) :
need at least two non-NA values to interpolate
I see that one of the errors has been mentioned in one other post here, although it does not answer the question of how to resolve the problem.
Am I using the command right? I am having hard time understanding if bsseq has options to handle single replicate data. If it can, which steps/options require changes? The documentation does not mention any special options for single replicate data and many times we prefer to add the data from replicates into single files per sample.
Thank you very much in advance.
R version 3.0.2 (2013-09-25)
Platform: x86_64-w64-mingw32/x64 (64-bit)
 LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
 LC_TIME=English_United States.1252
attached base packages:
 parallel stats graphics grDevices utils datasets methods base
other attached packages:
 bsseq_0.10.0 matrixStats_0.14.0 GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.7 BiocGenerics_0.8.0
loaded via a namespace (and not attached):
 Biobase_2.22.0 colorspace_1.2-4 grid_3.0.2 lattice_0.20-23 locfit_1.5-9.1 munsell_0.4.2 plyr_1.8.1 Rcpp_0.11.4 scales_0.2.4
 stats4_3.0.2 tools_3.0.2