PMetaData: PMetaData

In Sautie/MALDITOFSpectraPA: Processing and analysis of MALDI_TOF spectra

Description

extracts from csv files the taxonomic identifications of the isolates and transforms them according to the values of the scores

Usage

PMetaData(
  Dirp,
  fileout = "expMax.csv",
  fu = "max",
  y = 2,
  id = "NRI",
  sc = c(1, 8, 13, 18, 23, 28, 33, 38, 43, 48, 53),
  spNames = c(1, 5, 10, 15, 20, 25, 30, 35, 40, 45, 50)
)

Arguments

Dirp:	directory (and path) where the csv files are located,
fileout:	name of the output file where Maldi identifiers and species names are found,
fu:	this parameter determines whether only one of the scores (y, default value=2) is considered, or instead, the mean, median, minimum or maximum of the scores corresponding to each of the isolates, "means", "medians", "select", "max" and "min",
id:	determine whether unidentified isolates are labeled with "NRI" (default value) or removed ,
sc:	columns containing the scores spNames:columns containing the names of the identified species

Value

dataframe (and csv file) with three columns: Maldi identifiers, isolate identifications and the corresponding scores

Examples

Rn<-PMetaData("Bees project 2019-2020"), Rn<-PMetaData("Bees project 2019-2020", fileout="expMeans.csv", fu="means")
          Rn<-PMetaData("Bees project 2019-2020", fileout="expMedians.csv", fu="medians")

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