preproc: preproc

In pezzcvd/daphneg2:

Description

The function proprocesses data for GWAS analysis. It distinguishes among five different modes of preprocessing. Two of them target the univariate analysis: "E" for environmental target parameter and "P" if the target is phenotypical. THe latter three start a multivariate analysis: "PxP" phenotype target and phenotype covariate, ExE for environmental target and environmental covariate and "PxE" for phenotypical target and environmental covariate respectively.

Usage

preproc(
  pp.par,
  pp.option,
  pp.geno,
  pp.cvt = NULL,
  pp.loco = F,
  pp.pw = normalizePath("~")
)

Arguments

pp.par	character. Name of the parameter of interest.
pp.option	character. Label for which kind of analysis is needed (P, E, PxP, ExE, PxE)
pp.geno	character. Rdata file with genotype information.
pp.cvt	character. Name of the covariate. (default NULL)
pp.loco	boolean. Leave one chromosome out approach. (default FALSE).
pp.pw	character. Output path. (default home folder).

Value

NULL. It strarts the preprocessing prodedure and it calls either "univariate" or "multivariate" in order to produce GWAS files.

Examples

gen = system.file("extdata", "example_geno.RData", package = "daphneg2")
preproc("CO_Spring", "E", gen)

pezzcvd/daphneg2 documentation built on Oct. 13, 2021, 10:34 p.m.