In chasemc/IDBac_App: MALDI-TOF MS Protien and Small Molecule Analysis

knitr::opts_chunk$set(echo = TRUE)

Summary statistics

if (!inherits(pool, "Pool")) {
  stop("Must be pool")
}
if (length(pool > 1L)) {
  stop("Pool must be length = 1")
}

Plot of full dendrogram submitted for prioritization:

plot(param$dendrogram,
     horiz = T)

paste0("Number of samples in the full dendrogram: ", attributes(a)$members)

prioritization_results <- IDBacApp::prioritizer(pool = param$pool,
                                                dendrogram = param$dendrogram,
                                                h = param$p_cut,
                                                k = NULL,
                                                percent_metabolite_peaks = param$s_perc_retain,
                                                small_mol_peakPercentPresence = param$s_peak_perc,
                                                small_mol_lowerMassCutoff = param$s_min_cut,
                                                small_mol_upperMassCutoff = param$s_max_cut,
                                                small_mol_SNR = param$s_snr,
                                                tolerance = 0.002)

Full Dendrogram

• Showing cut line

chasemc/IDBac_App documentation built on Dec. 20, 2024, 9:08 p.m.