Running CODEX2 more than 1 chromosome

[Jones, Thomas]

Hello, 

I am a masters student at UCL and am using CODEX2 to investigate germline copy number variation in TCGA patients. Regarding the following code in the demo, could you please suggest how would it need to be changed in order to run CODEX on all the chromosomes within a sample? Is it a case of creating a loop, so performing CODEX on each chromosome individually? Or is it possible to have "chr" so it creates a "chr.index" containing all the chromosomes within the sample?

chr <- 20 # This can be run for one chromosome or multiple chromosomes
chr.index <- which(seqnames(ref_qc)==chr)
normObj.null <- normalize_null(Y_qc = Y_qc[chr.index,],
                               gc_qc = gc_qc[chr.index],
                               K = 1:5, N = N)

Apologies if there is an obvious answer to this, bioinformatics is still very new to me! 

Kind regards,

Thomas Jones