Entering edit mode
17 months ago
I am using the bioconductor package conumee for copy number variation in R. I've been able to apply the functions to my own data, but I don't understand the output of CNV.write(., what = "segments") completely. Specifically, I see NAs in the b-statistic column and p-value column. What does this indicate? Should these results be disregarded?
The output of CNV.write(x, what = "segments")
(as in vignette, but on new data) gives:
ID chrom loc.start loc.end num.mark bstat pval seg.mean seg.median
205549610159_R02C01 chr12 172870 133795948 1328 NA NA -0.024 -0.025
205549610159_R02C01 chr13 19450000 115079939 708 NA NA -0.018 -0.015
205549610159_R02C01 chr14 20175000 107269770 874 NA NA 0.008 0.009
205549610159_R02C01 chr15 20500000 22548097 7 7.952065 3.137163e-13 0.323 0.297
205549610159_R02C01 chr15 22723097 102435696 912 NA NA -0.026 -0.022`