mppR: create.mppData – R documentation

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mppR

create.mppData

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)

mppR

Multi-Parent Population QTL Analysis

v1.2.1

GPL-3

Authors

Vincent Garin [aut, cre], Valentin Wimmer [aut], Dietrich Borchardt [ctb, dtc], Fred van Eeuwijk [ctb, ths], Marcos Malosetti [ctb, ths]

Initial release

2020-02-10

create.mppData

Description

Usage

Arguments

Value

Author(s)

Examples

mppR

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