Copykat pipeline

This pipeline runs Copykat and adds a subsequent calling step that can call chromosome arm level alterations in individual cells

How to run

Mandatory parameters

Rscript copykat_pipeline.R
	-c [counts matrix]
	-g [chromosome coordinates]
	-o [output directory]

Recommended parameters - maually specify which cells to use as completely normal

        -l [File with aneuploid/diploid labels per cell with column names cell.names
                (barcodes) and copykat.pred (diploid or aneuploid)]

Optional parameters for additional plots

	-u [UMAP coordinates (colnames UMAP_1 and UMAP_2), with further possible annotations 
		of columns named cluster and/or celltype]

Dependencies

The pipeline has been tested with R version 4.1.1

optparse
copykat
tidyr
gtools
ggplot2
cowplot