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imminfo / tcr

[DEPRECATED, see https://immunarch.com/] tcR: an R package for immune receptor repertoire advanced data analysis.
https://immunarch.com/
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Regarding count.frame #22

Closed joonlee3 closed 9 years ago

joonlee3 commented 9 years ago

Hi,

When I use a function 'count.frames', should the sum of # of in-frame and out-of-frame sequences be equal to # of all sequences? For example, from my analysis, I found out that

count.frames(tcr_mm[[1]], 'all')
[1] 1223 count.frames(tcr_mm[[1]], 'in')
[1] 1166 count.frames(tcr_mm[[1]], 'out')
[1] 52

I thought that count.frames(tcr_mm[[1]], 'out') + count.frames(tcr_mm[[1]], 'in') = count.frames(tcr_mm[[1]], 'all')

Did I miss something? Please let me know.

Thanks, Joon

vadimnazarov commented 9 years ago

Hi Joon,

there is a parameter .coding that could affect the results. By default it's TRUE that means that only coding sequences (i.e., without stop-codon) will be returned as a result. You may take a look at the help page ?count.frames to see this parameter.