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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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importing mixcr dataset via tcR #79

Closed zuta-osa77 closed 8 years ago

zuta-osa77 commented 8 years ago

hi all,

I'm new to this: I've run mixcr/1.8.1 on my RNA-seq dataset using the partialAssemble workflow described on the main page and would like to create the analog of the twa list object in R which represents the Cloneset. I have several questions:

1) I'm guessing I need to run exportClones with a couple of specified fields in order to use

parse.mitcr

directly on it. Is this correct? If so, would anybody have the exact call to exportClones which would allow the output to be directly input into a Cloneset object in R? I don't know in other words how twa or twb were generated or cherrypicked from exportClones output

2) Along the same lines, how do I combine all the exportClones output from mixcr so that I can represent my entire dataset in a Cloneset, e.g. all four subjects are in twa

Basically, if there was a concrete example of how to go from N clns files (from mixcr assemble) to N exportClones files with the right fields picked out to be directly input into tcR, and then make a N x 1 list containing the entire dataset in a Cloneset object, that would be great!

Looks like a great set of routines and visualization scripts, so I can't wait to use it.

all the best, zo

vadimnazarov commented 8 years ago

Hi,

1) You should use parse.mixcr in order to parse the MiXCR files. Yes, first you run exportClones, and after that you parse the output files to R with parse.mixcr. I think you could just run mixcr exportClones clones.clns clones.txt, i.e., without any parameters, to get the suitable for tcR output tables.

2) You just need to put all your clns files to the same folder, and after that run your_list = parse.folder(path_to_your_folder, "mixcr"). Run ?parse.folder for more info.

I hope this helps. If not please message me here or by email.

zuta-osa77 commented 8 years ago

hey thanks Vadim

On Wed, Aug 10, 2016 at 1:08 PM, Vadim Nazarov notifications@github.com wrote:

Hi,

1) You should use parse.mixcr in order to parse the MiXCR files. Yes, first you run exportClones, and after that you parse the output files to R with parse.mixcr. I think you could just run mixcr exportClones clones.clns clones.txt, i.e., without any parameters, to get the suitable for tcR output tables.

2) You just need to put all your clns files to the same folder, and after that run your_list = parse.folder(path_to_your_folder, "mixcr"). Run ?parse.folder for more info.

I hope this helps.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/imminfo/tcr/issues/79#issuecomment-238934718, or mute the thread https://github.com/notifications/unsubscribe-auth/AT9_A84Wogfv1LgRnlMxJQxAha9vdkUgks5qegV0gaJpZM4Jgr90 .

vadimnazarov commented 8 years ago

No problems, please let me know if it works for you or not, so I would be able to help you / close this issue.

zuta-osa77 commented 8 years ago

Yes this worked out, thanks again for your help. I have another related question concerning filtering this imported dataset -- would you prefer in the interests of good organization that I open a new issue, ask you this in private, or just ask here?

vadimnazarov commented 8 years ago

Nice! Regarding another question - please, either open a new issue or send me an email, which way is more comfortable for you.