compare_k_vals: Compare k values

In campbio/musicatk: Mutational Signature Comprehensive Analysis Toolkit

Compare k values

Description

Compare the stability and error of various k values to help determine the correct number of signatures (k).

Usage

compare_k_vals(
  musica,
  modality,
  reps = 100,
  min_k = 1,
  max_k = 10,
  error_type = "prop",
  algorithm = "nmf"
)

Arguments

musica	A musica object.
modality	The modality to use, either "SBS96", "DBS78", or "IND83".
reps	Number of times prediction is performed. For each replicate, the count table data is perturbed. Multiple replicates allows for stability analysis by calculating silhouette width on the multiple results. Default 100.
min_k	Lower range of number of signatures for discovery. Default 1.
max_k	Upper range of number of signatures for discovery. Default 10.
error_type	Whether to calculate reconstruction error by proportions ("prop") or raw counts ("raw"). Default "prop".
algorithm	Algorithm for signature discovery. Default "nmf".

Value

a data.frame with stats for each k value tested

Examples

data(musica)
compare_k_vals(musica, "SBS96", reps = 3, min_k = 1, max_k = 5)

campbio/musicatk documentation built on Dec. 25, 2024, 9:34 p.m.