I'm trying to cluster scCNV data from 10X Genomics by clone using Adegenet's DAPC. I'm following the method in this paper and the R code to generate a CNV mutation matrix is provided in the supplement. However, it isn't clear to me how to input this matrix into Adegenet. Does anyone have any advice on how to do this or any alternatives to the matrix to use as input?
https://www.biorxiv.org/content/biorxiv/early/2019/09/05/757211.full.pdf
https://www.biorxiv.org/content/10.1101/757211v1.supplementary-material
matrix
seqnames start end width strand node ploidy qual event
5 20001 46400000 46380000 * cell_0 2 18 31
2 20001 84480000 84460000 * cell_0 3 18 71
17 20001 22240000 22220000 * cell_0 3 16 65
5 20001 46400000 46380000 * cell_1 2 19 31
2 20001 33120000 33100000 * cell_1 3 18 73
5 20001 46400000 46380000 * cell_10 2 18 31
2 20001 87060000 87040000 * cell_10 3 18 71
5 20001 46400000 46380000 * cell_100 2 19 31
2 20001 33140000 33120000 * cell_100 3 18 73
5 20001 46400000 46380000 * cell_1003 2 18 31
2 20001 87060000 87040000 * cell_1003 3 17 71
17 20001 22240000 22220000 * cell_1003 3 16 65
5 20001 46400000 46380000 * cell_1004 2 18 31
5 20001 46400000 46380000 * cell_1005 2 19 31
5 20001 46400000 46380000 * cell_1006 2 17 31
2 20001 87060000 87040000 * cell_1006 3 17 71
5 20001 46400000 46380000 * cell_1007 2 18 31
17 20001 22240000 22220000 * cell_1007 3 16 65
2 20001 87060000 87040000 * cell_1008 3 18 71
17 20001 22240000 22220000 * cell_1008 3 16 65
2 20001 87060000 87040000 * cell_1009 3 18 71
5 20001 46400000 46380000 * cell_101 2 19 31
2 20001 33140000 33120000 * cell_101 3 18 73
2 20001 87060000 87040000 * cell_1010 3 17 71
5 20001 46400000 46380000 * cell_1011 2 18 31
5 20001 46400000 46380000 * cell_1012 2 18 31
2 20001 87060000 87040000 * cell_1012 3 18 71
17 20001 22240000 22220000 * cell_1012 3 16 65
5 20001 46400000 46380000 * cell_1013 2 18 31
2 20001 87060000 87040000 * cell_1013 3 18 71
5 20001 46400000 46380000 * cell_1014 2 17 31
17 20001 22240000 22220000 * cell_1014 3 16 65
5 20001 46400000 46380000 * cell_1016 2 19 31
17 20001 22240000 22220000 * cell_1016 3 16 65
2 20001 87060000 87040000 * cell_1019 3 17 71
17 20001 22240000 22220000 * cell_1019 3 16 65
5 20001 46400000 46380000 * cell_102 2 18 31
17 20001 22240000 22220000 * cell_102 3 16 65
5 20001 46400000 46380000 * cell_1020 2 18 31
5 20001 46400000 46380000 * cell_1021 2 18 31
2 20001 87060000 87040000 * cell_1022 3 18 71
17 20001 22240000 22220000 * cell_1023 3 16 65
17 20001 22240000 22220000 * cell_1024 3 16 65
5 20001 46400000 46380000 * cell_1026 2 18 31
17 20001 22240000 22220000 * cell_1026 3 16 65
5 20001 46400000 46380000 * cell_1027 2 18 31
2 20001 87060000 87040000 * cell_1027 3 18 71
5 20001 46400000 46380000 * cell_1028 2 18 31
2 20001 33080000 33060000 * cell_1028 3 17 73
17 20001 22240000 22220000 * cell_1029 3 16 65
2 20001 87060000 87040000 * cell_103 3 18 71
