Tracking a list of target immune receptors across repertoires

Source: R/aaa_temp-receptor.R

Tracking a list of target immune receptors across repertoires

receptor_track(
  idata,
  targets,
  idata_col,
  targets_col,
  method = c("exact", "hamm", "lev"),
  max_dist = 2
)

– TRACK –

If no seq_options passed than seq_options is created automatically and takes the first column from the targets

  1. receptor_track Find receptors of interest 1a) List of CDR3 - vector + col to match (screw that, just pass a data frame) 1b) List of CDR3 + other columns 1c) List of CDR3 alpha + CDR3 beta (+ other columns) 2a) Find abundance of found receptors in an ordered repertoires 2b) Find abundance of receptors close by distance in an ordered repertoires 3a) Visualise via alluvial 3b) Compute PCA on abundances and visualise

Example: visualise the size of cell clusters those receptors belong to across different therapy time points