collapseClones unused argument "fields"
Issue #156
resolved
Greetings,
We are trying to use collapseClones including the “fields“ argument to avoid combining clones from different samples. Unfortunately we keep getting the same error:
collapseClones(db, cloneColumn = "clone_id", sequenceColumn = "sequence_alignment", germlineColumn = "germline_alignment_d_mask",
+ method = "thresholdedFreq", minimumFrequency = 0.6, includeAmbiguous = FALSE,
+ breakTiesStochastic = FALSE, nproc = 32, fields = c("sample_id"))
Error in collapseClones(db, cloneColumn = "clone_id", sequenceColumn = "sequence_alignment", :
unused argument (fields = c("sample_id"))
Execution halted
We tried naming the fields in different ways but couldn’t make it work.
Best wishes.
Comments (4)
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reporter You are totally right! It was the version. Sorry!
Thanks for your help!
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Great! Glad this fixed it.
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- changed status to resolved
Using older version
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Hi Carolina,
Could you verify that you’re using the most recent version of Shazam (1.1.0)? I believe this option wasn’t present in older versions. It seems to work on my setup with example data.
Best,
-Ken