reipatho
commented
1 year ago I solved my own problem I guess it is a kind of bug (or my poor understanding) First Tumor_ID and ccf.list.order should be aligned Following is my example
"KS01.clin" Tumor_Sample_Barcode Tumor_ID Patient_ID Tumor_Sample_Label KS01-1 D KS01 D_1 KS01-2 D KS01 D_2 KS01-3 S KS01 S_3 KS01-5 S KS01 S_5 KS01-6 D KS01 D_6
ccf.list <- compareCCF(maf, pairByTumor = TRUE, min.ccf = 0.02, use.adjVAF = TRUE, use.indel = TRUE)
KS01_S_D <- ccf.list$FJ01$**S-D**
KS01_S_D
result: NULL
ccf.list <- compareCCF(maf, pairByTumor = TRUE, min.ccf = 0.02, use.adjVAF = TRUE, use.indel = TRUE)
KS01_S_D <- ccf.list$KS01$**D-S**
KS01_S_D
result:
Hugo_Symbol Mut_ID D S
1 CASZ1 1:10660197:G:A 0.961 0.999
2 PRAMEF12 1:12775647:G:A 1.000 0.855
3 IGSF21 1:18365400:C:T 1.000 0.999
4 RHCE 1:25392020:G:A 1.000 0.999
5 AHDC1 1:27547288:G:A 0.963 0.999
Hello.
Now I'm analyzing Pairwise CCF comparison, and SOME (not all) cases are in stuck.
graphics::smoothScatter(matrix(c(KS01_S_D[, 3], KS01_S_D[, 4]),ncol = 2), xlim = c(0, 1), ylim = c(0, 1), colramp = colorRampPalette(c("white", RColorBrewer::brewer.pal(9, "BuPu"))), xlab = "S", ylab = "D") *KS01(sample name), S and D (position)
and return an error on "graphics::smoothScatter(matrix(c(KS01_S_D[, 3], KS01_S_D[, 4]),ncol = 2)", 'data' is 'NULL'
What should I do ?? And what is the difference among success cases and not ??