collapseClones unused argument "fields"

[Carolina Monzó]

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.

[Kenneth Hoehn]

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

[Carolina Monzó]

You are totally right! It was the version. Sorry!

Thanks for your help!

[Kenneth Hoehn]

Great! Glad this fixed it.

[Kenneth Hoehn]

Using older version