ABSOLUTE warning on cbs output

Question

[arshiaurora]

Hi,

I am running ABSOLUTE on a cbs input file without the maf option. I get the following warning:

In if (!is.na(res)) { ... :
the condition has length > 1 and only the first element will be used

I also get ploidy of an order of 7.(which is not expected) Can anyone help me with the warning ?

[poisonAlien]

What are your arguments to RunAbsolute? If you are using segmented data from cbs, copy_num_type argument should be set to total.

[arshiaurora]

Parameter to copy_num_type is set to total only. Here are the rest of the parameters.

sigma.p <- 0
max.sigma.h <- 0.02
min.ploidy <- 0.95
max.ploidy <- 10

primary.disease<-"kidney"
platform<-'Illumina_WES'

max.as.seg.count <- 1500
max.neg.genome <- 0
max.non.clonal <- 0
copy_num_type <- "total"

min.mut.af<-0