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sztup / scarHRD

MIT License
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question about TAI #22

Open sheny-bio opened 3 years ago

sheny-bio commented 3 years ago

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 commented 3 years ago

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

menzel commented 3 years ago

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)