modify.data: Function to modify genotype and phenotype data to match

In RAINBOWR: Genome-Wide Association Study with SNP-Set Methods

Function to modify genotype and phenotype data to match

Description

Function to modify genotype and phenotype data to match

Usage

modify.data(
  pheno.mat,
  geno.mat,
  pheno.labels = NULL,
  geno.names = NULL,
  map = NULL,
  return.ZETA = TRUE,
  return.GWAS.format = FALSE
)

Arguments

pheno.mat	A n _ 1 \times p matrix of phenotype data. rownames(pheno.mat) should be genotype (line; accesion; variety) names.
geno.mat	A n _ 2 \times m matrix of marker genotype data. rownames(geno.mat) should be genotype (line; accesion; variety) names.
pheno.labels	A vector of genotype (line; accesion; variety) names which correpond to phenotypic values.
geno.names	A vector of genotype (line; accesion; variety) names for marker genotype data (duplication is not recommended).
map	Data frame with the marker names in the first column. The second and third columns contain the chromosome and map position.
return.ZETA	If this argument is TRUE, the list for mixed model equation (ZETA) will be returned.
return.GWAS.format	If this argument is TRUE, phenotype and genotype data for GWAS will be returned.

Value

$geno.modi

The modified marker genotype data.

$pheno.modi

The modified phenotype data.

$ZETA

The list for mixed model equation (ZETA).

$pheno.GWAS

GWAS formatted phenotype data.

$geno.GWAS

GWAS formatted marker genotype data.

RAINBOWR documentation built on July 4, 2024, 1:11 a.m.