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Peak clustering

Source: R/nmr_peak_clustering.R
nmr_peak_clustering.Rd

Peak clustering

Usage

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))