Peak clustering — nmr_peak_clustering • AlpsNMR

Peak clustering

nmr_peak_clustering(
  peak_data,
  peak2peak_dist = NULL,
  num_clusters = NULL,
  max_dist_thresh_ppb = NULL,
  verbose = FALSE
)

Arguments

peak_data: The peak list
peak2peak_dist: The distances obtained with nmr_get_peak_distances. If NULL it is computed from peak_data
num_clusters: If you want to fix the number of clusters. Leave NULL if you want to estimate it
max_dist_thresh_ppb: To estimate the number of clusters, we enforce a limit on how far two peaks of the same cluster may be. By default this threshold will be computed as 3 times the median peak width (gamma), as given in the peak list.
verbose: A logical vector to print additional information

Value

A list including:

The peak_data with an additional "cluster" column
cluster: the hierarchical cluster
num_clusters: an estimation of the number of clusters
num_cluster_estimation: A list with tables and plots to justify the number of cluster estimation

Examples

peak_data <- data.frame(
    NMRExperiment = c("10", "10", "20", "20"),
    peak_id = paste0("Peak", 1:4),
    ppm = c(1, 2, 1.1, 2.2),
    gamma_ppb = 100
)
clustering_result <- nmr_peak_clustering(peak_data)
peak_data <- clustering_result$peak_data
stopifnot("cluster" %in% colnames(peak_data))