question about TAI

[sheny-bio]

I read the source code for the TAI section and have some question:

1. why ploidy = A_CN(longest segment)
2. why:
   if(!ploidy %in% c(1,seq(2, 200,by=2))){
   sample.seg[,'AI'] <- c(0,2)[match(sample.seg[,7] + sample.seg[,8] == ploidy & sample.seg[,7] != ploidy, c('TRUE', 'FALSE'))]
   }

[sheny-bio]

is No.6 column is TCN? but No.6 column in test_2.txt is A_CN

[menzel]

is No.6 column is TCN? but No.6 column in test_2.txt is A_CN

The columns are changend in line 45 to 49 in scar_score.R
So they are ¨correct" at this step (the column headers remain the same and are wrong by then)