Improve documentation describing day0 label

[jeremymsimon]

Description of feature

I've read the crisprseq and MAGeCK documentation a few times and the description and function of the day0_label is still a bit unclear to me, both in terms of how it should be specified (especially if there are multiple control samples/replicates) and what specifically it does.

Let's say I have 3 control samples, and 3 treated samples, should the day0_label be set to control as is specified in my contrasts? Or should it be a comma-separated list of e.g. Control_Rep1,Control_Rep2,Control_Rep3? Or is it only appropriate for a true time-course experiment?

Further, according to the MAGeCK documentation the day0 label is a required parameter, but it does not seem to be required for crisprseq to run--I get MAGeCK counts and MLE results regardless. Is it figuring out a label automatically based on the contrasts, or is this a bug?

Thanks!

[LaurenceKuhl]

Hi @jeremymsimon this is normally now more thoroughly described, if you still find it confusing feel free to re open this issue :)