CARD_SCMapping

[lindsdudley]

Hi developers,

Thank you so much for developing this helpful tool. I am extremely interested in you SC mapping function. I have a deconvoluted CARD object with single cell reference that works for all of the visualizations in the tutorial but when I attempt to extend that to the SCMapping function I encounter an error. This is the line of code that I use:

scMapping = CARD_SCMapping(CARD_obj,shapeSpot="Square",numCell=20,ncore=10)

and this is the error I recieve:

Error in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 20, 0
In addition: Warning message:
In asMethod(object) :
sparse->dense coercion: allocating vector of size 2.3 GiB

I am running this on a high powered Linux machine running POP OS. Please let me know if you have any insight into how to resolve this error. Thank you again for your help!

[lindsdudley]

Hi @YingMa0107 I would still love to hear your thoughts on this as i haven't been able to figure it out. I am also hoping to use a cell to cell communication program on this data and I would like to know the best way to extract the matrix of data information that I can use as input for that. Ideally after I get scMapping to work as I would like to do it at the psuedo single cell level. Thank you so much for creating such a helpful program and Go Blue!