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Use already annotated files (.trn files from the BAS software)

BAS tags in FLightR

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#1 PetraQ

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Posted 06 February 2018 - 04:50 AM

Hi,
I'm interested in re-processing some BAS tag data anotated previously with BAS software in FLightR.

I would be very grateful if anybody can help me with this question:
Has anybody used some function/script to read the .lig and .trn files generated previously with BAS software to the TAGS format?

 

Thank you very much!

Petra



#2 L Halpin

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Posted 06 February 2018 - 06:51 PM

Hi Petra,

 

You should be able to import .lig files using the readLig command in the package TwGeos 

 

For processing this might help: 

 

https://www.rdocumen...ics/BAStag2TAGS



#3 PetraQ

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Posted 07 February 2018 - 01:35 PM

Hi,

thank you, but unfortunately this is not the solution to my question, as I also need to import the annotation (.trn) files, and there is no function for this. I would like to use the same annotation as before, to compare the outputs based on the same criteria, and without spending long times annotating previous datasets again.

Cheers,

Petra



#4 L Halpin

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Posted 07 February 2018 - 08:17 PM

To the best of my knowledge, you can't open .trn files or other previously defined twilights, in the the various functions that define twilights.  I have always had to go back in and redefine them.  However, someone else may have a better response.

 

This twilight-free method may be of interest, but I haven't tested it on any of my data yet:

http://onlinelibrary....12953/abstract



#5 PetraQ

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Posted 08 February 2018 - 09:18 AM

Hi,

thank you, I found it, it works like this:

 

library(GeoLight)
transitions <- trnTrans("MK10_21510_Reconstructed_000.trn")
raw <- ligTrans("MK10 21510 Reconstructed_000.lig")

library(FLightR)
GeoLight2TAGS(raw=raw, gl_twl=transitions, threshold=10, filename = "prion21510.csv")
Prion.data<-get.tags.data("prion21510.csv")

 

cheers,

Petra






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