Retrieving mixscale scores for NT cells

[robinfallegger]

Hi, thanks for the great package!

I was wondering how to retrieve the mixscale scores for the cells without targeting guides (NT) as you show in Figure 2c of the preprint ? Currently, they are always exactly 0

Thanks in advance for your help!

[longmanz]

Hi @robinfallegger ,
Sorry for the late reply and thank you for using our package!

To retrieve the raw Mixscale scores for every cell, you can use the following commands:

prtb_score <- Tool(object = object, slot = "RunMixscale")

The scores are stored as a list of many data frames(prtb_score) according to their target gene + cell type identity. However, please be aware that the scores for the NT cells will not be unique, because NT cells are re-used when calculating the scores for each target gene. Therefore, you will need to know first decide which target gene you are interested in, and then extract the corresponding data frame from this list.