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sartorlab / methylSig

R package for DNA methylation analysis
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CT SNP filtering does not work properly #1

Closed rcavalcante closed 9 years ago

rcavalcante commented 9 years ago

CT SNP GRanges object has start = end and is 1-based. Input data from methylKit and from Bismark is 1-based. However, findOverlaps(...) is still not finding all the locations of C > T SNPs in the methylation data.

rcavalcante commented 9 years ago

Realized that I neglected to pass filterSNPs parameter from readBismarkData(...) and methylSigReadData(...) to their helper functions.