SPCA: SPCA

In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

Description

function for Principal Component Analysis of Maldi_Tof spectra with external clusters based on metadata information

Usage

SPCA(
  df_m,
  varCat1,
  value,
  varCat2,
  contDim = TRUE,
  contVar = FALSE,
  contInd = FALSE
)

Arguments

df_m:	dataframe containing peaks and metadata
varCat1:	categorical variable for choosing isolates, examples: "Taxonomie" ,"Genre", "Date.d.analyse" ,"Origine","Ruche", "Nutrition" , "Date.de.récolte" , "Lieu.de.la.ruche"
value:	level of catVar1, examples: "Lactobacillus" ("Genre"), Taxonomie("Pediococcus pentosaceus"), "Erica cinerea" ("Nutrition"),...
varCat2:	categorical variable for partitioning the chosen isolates, examples: Taxonomie, Genre, Date.d.analyse, Origine, Ruche, Nutrition, Date.de.récolte, Lieu.de.la.ruche
contDim:	graph and statistics for PC contributions (default, contDim=TRUE)
contVar:	graph and statistics for variable contributions(default,contVar= FALSE)
contInd:	graph and statistics for isolate contributions (default, contInd=TRUE)

Examples

      hg<-SPCA(df_Peaks, varCat1="Genre", value="Lactobacillus", varCat2="Nutrition")

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