Repeated Start fields in choose_TSS.R (Lines 112-120)

[zhang-jiankun]

Dear Engreitz group,

Thank you for developing the ABC prediction model. I’ve been going through the code in the choose_TSS.R script, and I was wondering if there might be an issue with lines 112-120:

end.this = if_else(L1.full$strand[j]=="+", ceiling((L1.full$end[j]+L1.full$end[j+1])/2) , ceiling((L1.full$TSS[j]+L1.full$TSS[j+1])/2))

start.this = if_else(L1.full$strand[j]=="+", ceiling((L1.full$TSS[j]+L1.full$TSS[j+1])/2),ceiling((L1.full$end[j]+L1.full$end[j+1])/2))
geneFile = rbind(geneFile, c(chr=L1.full$chr[j], start=ceiling(L1.full$TSS[j]+L1.full$TSS[j+1])/2,
TSS=ceiling((L1.full$TSS[j]+L1.full$TSS[j+1])/2),
end=end.this, start=start.this, gene=goi, level=1,
strand=L1.full$strand[j], gene_type=L1.full$gene_type[j],
TSS=ceiling((L1.full$TSS[j]+L1.full$TSS[j+1])/2),
choice="Multiple close L1 TSSs"))

It looks like the "TSS" field is being repeated twice, and the "start" field is also repeated with different values. Might there be an issue here?

I’m not entirely sure if this is the intended behavior, so I wanted to check with you.

Best,

Jiankun