Sorry the error message is actually this: (I changed the number of samples >=2 to 1 briefly to check whether this was the problem)
Error in which(rowSums(BS.cov[, bsseq.data$Type == "SSA"] >= 2) >= 2 & :
error in evaluating the argument 'x' in selecting a method for function 'which': Error in rowSums(BS.cov[, bsseq.data$Type == "SSA"] >= 2) :
'x' must be an array of at least two dimensions
In addition when I look at the number of CpGs covered by at least 1 read in all samples I get only 151
sum(rowSums(getCoverage(bsseq.data) >= 1) == 14
[151]
Error in which(rowSums(BS.cov[, bsseq.data$Type == "SSA"] >= 2) >= 2 & :
error in evaluating the argument 'x' in selecting a method for function 'which': Error in rowSums(BS.cov[, bsseq.data$Type == "SSA"] >= 2) :
'x' must be an array of at least two dimensions
In addition when I look at the number of CpGs covered by at least 1 read in all samples I get only 151
sum(rowSums(getCoverage(bsseq.data) >= 1) == 14
[151]
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