Hi Rob, Thanks for your inquiry about the DECIPHER package. The behavior you describe is expected for the 'minInformation' parameter. It controls when to switch to the 'noConsensusChar'. The parameter that I think you are describing is 'threshold', which controls the amount of sequence information to maintain in each position. Using your example, here are some variants: > ConsensusSequence(DNAStringSet(c("A", "A", "A", "T"))) A DNAStringSet instance of length 1 width seq [1] 1 W > ConsensusSequence(DNAStringSet(c("A", "A", "A", "T")), threshold=0.3) A DNAStringSet instance of length 1 width seq [1] 1 A > ConsensusSequence(DNAStringSet(c("A", "A", "A", "T")), threshold=0.3, minInformation=0.8) A DNAStringSet instance of length 1 width seq [1] 1 + > ConsensusSequence(DNAStringSet(c("A", "A", "A", "T")), threshold=0.3, minInformation=0.8, noConsensusChar="N") A DNAStringSet instance of length 1 width seq [1] 1 N The first case is your example of three "A"s and a "T". The second case is what I think you want to do - get an "A" by dropping the "T". Then only 75% of the sequence information is maintained, so setting minInformation to 0.8 will trigger the 'noConsensusChar' (by default, "+"). This can be changed to an "N" as in the fourth example. I hope that helps answer your question. Erik On May 5, 2016, at 9:40 PM, rob.lanfear [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""/> User rob.lanfear<https: support.bioconductor.org="" u="" 9413=""/> wrote Question: Possible bug in ConsensusSequence<https: support.bioconductor.org="" p="" 82355=""/>: Hi there, I have a possible bug in ConsensusSequence, specifically that the minInformation parameter does not appear to work (at least in the way I understand it should from the documentation). For example, in an alignment of 4 sequences, where a given site has 3 A's and one T, I would expect that setting minInformation to 0.7 should return a consensus of an 'A', but setting it to 0.8 would return a consensus of 'W'. However, no matter what I do (including whether I set ambiguity to 'TRUE' or 'FALSE', I always get a 'W' here. Am I doing something wrong, or misunderstanding something? Or is this a bug? Thanks either way for an awesome package, Rob ________________________________ Post tags: DECIPHER You may reply via email or visit Possible bug in ConsensusSequence