I need help with how to modify the sbdry parameter in DNAcopy

Question

[mikki]

My group has used VarScan and DNAcopy for CNV analysis from Whole Exome Sequencing data, where the tumor sample was taken from FFPE. We are aware that it can be hard to get good results from FFPE samples, but would like to maximize the information we can get regardless, since that is the only available sample. However, we get kind of a weird result from segmentation - basically there are no copy number changes for most of the genome except for 2 very large segments (length ~ 86M and 36M) on chromosomes 15 and 22.

The unsegmented data appears to have areas of copy number change within very large segments with low segment mean. I've read through the documentation for DNAcopy and it appears that changing the'sbdry' parameter would limit how long the segments can grow, and possibly capture more granular copy number changes. However, I've been unable to find, in the documentation or elsewhere, what to change the 'sbdry' TO. I could use the 'getbdry' function to calculate them, but there is no guidance on how to change it's parameters to get more meaningful results. Can anyone provide any guidelines?

This was the code used: library(DNAcopy) cn <- read.table("your.cn.file",header=F) CNA.object <-CNA( genomdat = cn[,7], chrom = cn[,1], maploc = cn[,2], data.type = 'logratio') CNA.smoothed <- smooth.CNA(CNA.object) segs <- segment(CNA.smoothed, verbose=0, min.width=2) segs2 = segs$output write.table(segs2[,2:6], file="out.file", row.names=F, col.names=F, quote=F, sep="\t")

Thank you!

Answer 1

[ssv.bio]

library(DNAcopy)
data(coriell)
CNA.object <- CNA(cbind(coriell$Coriell.05296),
                  coriell$Chromosome,coriell$Position,
                  data.type="logratio",sampleid="c05296")
smoothed.CNA.object <- smooth.CNA(CNA.object)
sdundo.CNA.object <- segment(smoothed.CNA.object, 
                             undo.splits="sdundo", 
                             undo.SD=3,verbose=1, sbdry=default.DNAcopy.bdry)

---

 > str(default.DNAcopy.bdry)
     int [1:5151] 9500 8352 9864 7316 9174 9936 6473 8360 9474 9962 ...

Please read getbdry function in DNAcopy

[mikki]

Thank you! I read the documentation on getbdry and didn't find it helpful, but today found another page with appropriate starting values - https://rdrr.io/bioc/DNAcopy/man/getbdry.html