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rnabioco / djvdj

An R package to analyze single-cell V(D)J data
https://rnabioco.github.io/djvdj
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confusing `filter_paired` argument #117

Closed jayhesselberth closed 1 year ago

jayhesselberth commented 1 year ago

In the README, you have:

so <- import_vdj(
  input         = so,      # Seurat or SingleCellExperiment object
  vdj_dir       = paths,   # Cellranger output directories
  filter_paired = FALSE    # Only include clonotypes with paired chains
)

But I would expect that if you only want paired chains (i.e., you are filtering other things out) then you should set filter_paired = TRUE. Is the logic backwards? Or maybe the comment is inaccurate?

sheridar commented 1 year ago

'filter_paired = TRUE' will only include paired chains, so the comment is inaccurate