I use bsseq package for WGBS data analysis. After smoothing, I had tried to BSmooth.tstat for computing t-statistics. But BSmooth.tstat gave me following error.
bis.fit.you.tstat <- BSmooth.tstat(data, group1 = c("test", "test", "test") group2 = c("cont", "cont", "cont"), estimate.var = "paired", verbose = T, local.correct = TRUE, mc.cores=1) [BSmooth.tstat] preprocessing ... done in 30.6 sec [BSmooth.tstat] computing stats within groups ... done in 64.8 sec [BSmooth.tstat] computing stats across groups ... approxfun(xx, yy) : need at least two non-NA values to interpolate
I found that several CpG site methylation has NA. Does anyone know how to remove NA containing row from bisseq object?
Best Regards, Taiki