tlsR (version 0.1.2)

calc_icat: Calculate ICAT (Immune Cell Arrangement Trace) Index

Description

Quantifies linear/organized arrangement of cells within a TLS using FastICA.

Value

Numeric ICAT value.

Arguments

patientID

Character. Name of the sample in ldata.

tlsID

Numeric/integer. TLS identifier.

ldata

Named list of data frames (optional; defaults to global ldata).

Examples

data(toy_ldata)
ldata <- detect_TLS("ToySample", k = 30, ldata = toy_ldata)  # First detect TLS
if (max(ldata[["ToySample"]]$tls_id_knn) > 0) {
  icat <- calc_icat("ToySample", tlsID = 1, ldata = ldata)
  icat
}