RunTcrdist3

This function runs the tcrdist3 pipeline on a set of CDR3 sequences in a Seurat Object.

RunTcrdist3(
  seuratObj,
  organism = "human",
  chains = c("TRA", "TRB"),
  minimumCloneSize = 2,
  calculateChainPairs = FALSE,
  debugTcrdist3 = FALSE,
  verbose = FALSE
)

Arguments

seuratObj

The seuratObj containing formatted metadata

organism

Organism to use for tcrdist3. Default is 'human'.

chains

Vector of TCR chains to include in the analysis. Default is c("TRA", "TRB").

minimumCloneSize

Minimum number of clones per subject to include in the analysis. Default is 2.

calculateChainPairs

Boolean controlling whether to compute joint multi-chain distance matrices for observed chain combinations.

debugTcrdist3

Boolean controlling whether to run tcrdist3 in debug mode.

verbose

Boolean controlling whether to display processing steps.