Extend transformAssay so that it accepts multiple transformations at once?
In addition to
transformAssay(tse, ..., method="clr")
we could have
transformAssay(tse, ..., method=c("relabundance", "clr", "log10"), pseudocount=TRUE)
i.e. method could also be a vector.
Then pseudocount is something we would only like to apply to those transformations where it is really necessary. Here, not to relabundance but yes to clr and log10. One option would be to give that also as a vector, like pseudocount=c(FALSE, TRUE, TRUE).
Extend transformAssay so that it accepts multiple transformations at once?
In addition to
transformAssay(tse, ..., method="clr")we could have
transformAssay(tse, ..., method=c("relabundance", "clr", "log10"), pseudocount=TRUE)i.e. method could also be a vector.
Then pseudocount is something we would only like to apply to those transformations where it is really necessary. Here, not to relabundance but yes to clr and log10. One option would be to give that also as a vector, like pseudocount=c(FALSE, TRUE, TRUE).