mismatch of documentation and implementation regarding how to specify design for DESeq2.

[mschilli87]

The docstring claims design should be a formula when method="DESeq2":

muscat/R/pbDS.R

Line 13 in 49a3b32

#' For \code{"DESeq2"}, a formula with variables in \code{colData(pb)}.

However, pbDS calls .check_args_pbDS before considering method:

muscat/R/pbDS.R

Line 95 in 49a3b32

.check_args_pbDS(args)

That function immediately fails if design is anything but a matrix:

muscat/R/validity-checks.R

Lines 153 to 154 in 49a3b32

	if (!is.null(u$design))
	stopifnot(is.matrix(u$design),

So how would I run DESeq2 for ~ batch + group_id instead of the default ~ group_id?

[mschilli87]

I tried model.matrix(~ batch + group_id, as.data.frame(colData(sce)) and it seems to work (at least I didn't get any error).
However, at least the documentation should be fixed to make this clear. Ideally, I think this coulds (and probably should) be handled within pbDS. If you agree, I could check if this already handled and the validation is broken and provide a PR if you don't have time to look into this. In that case, please let me know.