Comments (5)
Hi,
-
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 withparse.mixcr
. I think you could just runmixcr exportClones clones.clns clones.txt
, i.e., without any parameters, to get the suitable for tcR output tables. -
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.
from tcr.
hey thanks Vadim
On Wed, Aug 10, 2016 at 1:08 PM, Vadim Nazarov [email protected]
wrote:
Hi,
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.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.
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from tcr.
No problems, please let me know if it works for you or not, so I would be able to help you / close this issue.
from tcr.
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?
from tcr.
Nice! Regarding another question - please, either open a new issue or send me an email, which way is more comfortable for you.
from tcr.
Related Issues (20)
- Problem parsing immunoseq for tcR package -- Error: Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : scan() expected 'an integer', got 'nodata' HOT 1
- parsing mixcr 3.0.3 file HOT 4
- Error when trying to parse data HOT 1
- Issue with name fixes HOT 1
- tcR conflict with other R packages?
- New immunoSEQ files won't parse. HOT 4
- pca.segments.2D
- plot "vis.gene.usage" by "Read.proportion" HOT 1
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- Differential abundance calculation? HOT 1
- Skipping files while parsing HOT 1
- Chao1 tcR
- signif.digits in vis.heatmap does not work as espected HOT 1
- importing mixcr dataset HOT 1
- TRBV6-8 and TRBV6-9 absence form the HUMAN_TRBV set HOT 1
- Names of gene segments in tcR HOT 1
- vis.rarefaction Warning: Ignoring unknown aesthetics: Group HOT 1
- Sample names in mixcr input HOT 1
- Cosine similiarity HOT 1
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