create.mppData: Create a multi-parent population data object

In vincentgarin/mppR: Multi-Parent Population QTL Analysis

Create a multi-parent population data object

Description

This function combines all raw data sources in a single data object of class mppData.

Usage

create.mppData(
  geno.off = NULL,
  geno.par = NULL,
  map = NULL,
  pheno = NULL,
  cross.ind = NULL,
  par.per.cross = NULL
)

Arguments

geno.off	Character marker score matrix of the offspring with genotypes as row and markers as column. Rows names must be the offspring genotypes identifiers similar to the one used in pheno. The columns names must be the marker names similar to the one used in map. Marker scores must be coded using one letter per allele. For example, AA, CC, GG, etc. Missing values must be coded NA.
geno.par	Character marker score matrix of the parents with genotypes as row and markers as column. Rows names must be the parents genotypes identifiers similar to the one used in par.per.cross. The columns names must be the marker names similar to the one used in map. Marker scores must be coded using one letter per allele. For example, AA, CC, GG, etc. Missing values must be coded NA.
map	Three columns data.frame with: 1) character marker identifiers; 2) numeric chromosome; 3) numeric positions in centi-Morgan.The marker identifiers must be identical to the column names of the maker matrices (geno.off and geno.par). The chromosome identifiers must start by 1 and increase by 1 unit, e.g. 1, 2, 3, ...
pheno	Numeric matrix with one column per trait and rownames as genotypes identifiers. The genotypes identifiers must be identical to the rownames of the offspring marker matrix (geno.off).
cross.ind	Character vector indicating to which cross each genotype belongs.
par.per.cross	Three columns Character matrix specifying : 1) the cross indicators; 2) the parents 1 identifiers of the crosses; 3) the parents 2 identifiers of the crosses. The list of crosses must contain the same cross indicators as in cross.ind and they must appear in the same order. The list of parent identifiers must be the same to the rownames of the argument geno.par.

Value

a list of class mppData which contains the following elements

geno.off	Matrix with offspring marker scores.
geno.par	Matrix with parents marker scores.
pheno	Matrix with phenotypic trait values.
map	Data.frame with genetic marker information.
cross.ind	Cross indicator.
par.per.cross	Character matrix information about cross and the parents of the crosses.

The list also contain other arguments that will be filled later in the data processing.

Author(s)

Vincent Garin

Examples

data(USNAM_geno)
data(USNAM_map)
data(USNAM_pheno)

geno.off <- USNAM_geno[7:506, ]
geno.par <- USNAM_geno[1:6, ]
map <- USNAM_map
pheno <-  USNAM_pheno
cross.ind <- substr(rownames(pheno), 1, 4)
par.per.cross <- cbind(unique(cross.ind), rep("B73", 5),
                       rownames(geno.par)[2:6])

mppData <- create.mppData(geno.off = geno.off, geno.par = geno.par,
                          map = map, pheno = pheno, cross.ind = cross.ind,
                          par.per.cross = par.per.cross)
                          

vincentgarin/mppR documentation built on March 13, 2024, 7:30 p.m.