BHclus: fBHclus

In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

Description

function wrapper of pvclust for building dendrograms labeled with bootstrap probabilities for isolates chosen according to varCat1 levels

Usage

BHclus(
  df_m,
  meth = "ward.D2",
  dist = "euclidean",
  varCat1,
  value,
  nb = 100,
  fig = TRUE,
  ni = 1,
  nf = 10
)

Arguments

ni, nf:	first and last columns corresponding to categorical variables (default values, ni=1, nf=10)
df_m:	dataframe containing peaks and metadata
meth:	hierarchical clustering algorithm ("ward2", default value), other values: "average", "ward.D", "single", "complete", "mcquitty", "median" or "centroid"
dist:	distance ("euclidean", default value), "maximum", "manhattan", "canberra", "binary" "correlation", "uncentered", "abscor"
varCat1:	categorical variable, example: "Genre","Taxonomie", " Nutrition", "Ruche"...
value:	value of catVar1 "Lactobacillus" ("Genre"), Taxonomie("Pediococcus pentosaceus"), "Erica cinerea" ("Nutrition"),...
nb:	n of bootstrap iterations (nb=100, default)
fig:	boolean variable to indicate output figure (fig=TRUE, default value)

Value

output cluster and figure

Examples

    dft<-BHclus(df_Peaks, varCat1="Genre", value="All", nb=500),
              dft<-BHclus(df_Peaks, varCat1="Genre", value="Lactobacillus", nb=500)
              dft<-BHclus(df_Peaks, varCat1="Taxonomie", value="Pediococcus pentosaceus"),
              dft<-BHclus(df_Peaks, meth="complete", dist="canberra",varCat1="Taxonomie", value="Pediococcus pentosaceus")
      source: https://academic.oup.com/bioinformatics/article/22/12/1540/207339
              https://www.rdocumentation.org/packages/pvclust/versions/2.2-0/topics/pvclust
              https://www.rdocumentation.org/packages/stats/versions/3.2.1/topics/dist

Sautie/MALDITOFSpectraPA documentation built on Dec. 31, 2020, 4:28 p.m.