Summarize Detected TLS Across Samples — summarize

Produces a tidy data.frame with one row per sample summarising the number of detected TLS, their sizes, and (optionally) ICAT scores.

Usage

summarize_TLS(ldata, calc_icat_scores = FALSE)

Arguments

ldata: Named list of data frames as returned by detect_TLS (and optionally detect_tic).
calc_icat_scores: Logical. Should ICAT scores be computed for each TLS and appended as a list-column? Default FALSE.

Value

A data.frame with columns:

sample: Sample name.
n_TLS: Number of TLS detected.
total_cells: Total cells in the sample.
TLS_cells: Number of cells assigned to any TLS.
TLS_fraction: Fraction of all cells that are TLS cells.
mean_TLS_size: Mean cells per TLS (NA if n_TLS = 0).
n_TIC: Number of T-cell clusters detected by detect_tic (NA if not yet run).
icat_scores: List-column of ICAT scores per TLS (only when calc_icat_scores = TRUE).

Examples

data(toy_ldata)
ldata <- detect_TLS("ToySample", k = 30, ldata = toy_ldata)
#> Detected TLS: 2
summarize_TLS(ldata)
#>      sample n_TLS total_cells TLS_cells TLS_fraction mean_TLS_size n_TIC
#> 1 ToySample     2      322951      1568  0.004855226           784    NA