pull.biomarkers: Extract the detected biomarkers from a population object.

In pheno2geno: High-Throughput Generation of Genetic Markers and Maps from Molecular Phenotypes for Crosses Between Inbred Strains

Description

Extract the detected biomarkers from a population object, or select biomarkers that best match a certain pattern.

Usage

  pull.biomarkers(population, pattern, verbose=FALSE)

Arguments

population	An object of class population. See create.population for details.
pattern	Vector containg pattern to be matched in markers.
verbose	Be verbose.

Details

After running generate.biomarkers function, biomarkers are stored inside population class object. Use the pull.biomarkers function to extract them from the popuklation object into a matrix. This will return a matrix will all the markers or when pattern is specified a vector with biomarkers best matching the pattern.

Value

Matrix of all markers / vector with markers best matching the specified pattern.

Author(s)

Konrad Zych [e-mail], Danny Arends [e-mail] Maintainer: Konrad Zych [e-mail]

See Also

• generate.biomarkers - Create genotype markers out of gene expression data.

• read.population - Load genotype, phenotype, genetic map data files into R environment into a population object.

• cross.denovo - Create de novo genetic map or vector showing how chromosomes should be assigned.

• cross.saturate - Saturate existing map.

• find.diff.expressed - Using Rank Product or student t-test analysis to select differentially expressed genes.

Examples

  data(testPopulation)
  markers <- pull.biomarkers(testPopulation,verbose=TRUE)
  bestMarker <- pull.biomarkers(testPopulation,round(runif(148)),verbose=TRUE)

pheno2geno documentation built on May 2, 2019, 6:35 a.m.