Unsure about the real need of this

[SamGG]

Hi Helena,
While adapting prepData() to convert my own object to sce and then using the CATALYST pipeline, I am usure about the need of this factor conversion

CATALYST/R/prepData.R

Lines 291 to 295 in 4ff7b02

	cd <- DataFrame(lapply(md[k], function(u) {
	v <- as.character(rep(u, md$n_cells))
	factor(v, levels = levels(u))
	}), row.names = NULL)

as md is reduced to the columns specified in md_cols and those columns previously converted to factor in

CATALYST/R/prepData.R

Lines 231 to 236 in 4ff7b02

	# assure correctness of formats
	k <- c(md_cols$id, md_cols$factors)
	md <- md[, k, drop = FALSE] %>%
	mutate_all(factor) %>%
	rename("sample_id" = md_cols$id)

In the latter part, I am also unsure about the rename at L235.

Could you have a look when you have time and just drop me a line (without explanation) if you modify something or not.
Best wishes,
Samuel