[BioC] consensusString Function

[Heidi Dvinge]

Hello Erik,

unfortunately I'm not familiar with the Biostrings package, so I can't
tell you why this doesn't work, but until someone else can answer, this
seems to be a work-around.

Apparently, consensusString doesn't handle Ns.

> test <- DNAStringSet(c("AANN","ACTG"))
> consensusString(test)
Error in .local(x, ...) :
  'threshold' must be a numeric in (0, 1/sum(rowSums(x) > 0)]

If there are no Ns things are okay though.

> test2 <- DNAStringSet(c("AAAA","ACTG"))
> consensusString(test2)
[1] "AMWR"

However, Ns seem acceptable if the consensus matrix is calculated first,
although they might result in ?s where no consensus could be found.

> test3	<- consensusMatrix(test)
> consensusString(test3)
[1] "A???"

HTH
\Heidi


> Hello,
>
> I am trying to get a consensus string for a DNAStringSet, but I am getting
> an error.  The documentation for consensusString says the argument "x" is
> either a consensus matrix or an XStringSet.  So this should work, right?:
>> myDNAStringSet <- DNAStringSet(c("NNNN","ACTG"))
>> consensusString(myDNAStringSet)
> Error in .local(x, ...) :
>   'threshold' must be a numeric in (0, 1/sum(rowSums(x) > 0)]
>
> Specifying a threshold in the arguments doesn't seem to make a difference.
>
> Thanks!,
> Erik
>
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