Copy number alteration from .bam files panelcn.mops

Question

[Pin.Bioinf]

Hello, I want to detect the copy number alterations among my 3 samples: Pre treatment sample, post treatment sample and metastasis sample.

I am using panelcn.mops package from R, which is for targeted sequencing. I have my bam files and the workflow needs a 'control' to be assigned in order to compare.

Is it good practice to do POST treatment vs PRE (using pre as control) and then Mutation vs PRE (using PRE as control, always) in this package? Am I supposed to do it like that?:

Sample code: ( doing a two sample comparison at a time: POST vs PRE or METAST vs PRE)

BAMFiles <- list.files(dir, pattern=".bam$", full.names=TRUE)


test <- countBamListInGRanges(countWindows = countWindows,
                              bam.files = BAMFiles, read.width = 150)


XandCB <- test
elementMetadata(XandCB) <- cbind(elementMetadata(XandCB[,1]), ### POST or METAST. sample
                                 elementMetadata(XandCB[,2])) ## PRE (control ??)

resultlist <- runPanelcnMops(XandCB,
                             testiv = c(1),        ## selecting POST or METAST. as test 
                             countWindows = countWindows)

Thank you