mppR: parent_cluster.mppData – R documentation

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parent_cluster.mppData

Parent clustering for mppData objects

Description

Integrate the parent clustering information to the mppData object. The parent clustering is necessary to compute the ancestral model. If the parent clustering step is skipped, the ancestral model can not be used but the other models (cross-specific, parental, and bi-allelic) can still be computed.

Usage

parent_cluster.mppData(mppData, par.clu = NULL)

Arguments

mppData

An object of class mppData. the mppData must have been processed using: create.mppData, QC.mppData, IBS.mppData, and IBD.mppData.

par.clu

Interger matrix representing the results of a parents genotypes clustering. The columns represent the parental lines and the rows the markers. The columns names must be the same as the parents list of the mppData object. The rownames must be the same as the map marker list of the mppData object. At a particular position, parents with the same value are assumed to inherit from the same ancestor. for more details, see par_clu. Default = NULL.

Details

At a single marker position, two parents can be grouped into a similar ancestral classes if we assume that they receive there allele from a common ancetor. The parent clustering information (par.clu) describe parental relatedness and which parent belong to which ancestral group. For example, at marker i, we could have five parents (pA, pB, pC, pD, pE) and the following clustering information (1, 2, 1, 2, 3). This means that pA and pC received their allele from the same ancetor (A1). pB and pD also have a shared ancestor (A2) who is different from (A1). And pE was not included in any group and can be seen as an indepedent ancestral group (A3).

The parent clustering information is provided via par.clu. It is an interger matrix with markers in row and parents in columns. At a particular marker position, parents with the same value are assumed to inherit from the same ancestor. for more details, see par_clu.

The parent clustering can be performed using the R package 'clusthaplo' that can be found there: https://cran.r-project.org/src/contrib/Archive/clusthaplo/. The 'clusthaplo' option is not integrated in this version of mppR. However, a version of mppR with function calling clusthaplo can be found on github https://github.com/vincentgarin/mppR (branch mppR_clusthaplo).

Value

An increased mppData object containing the the same elements as the mppData object provided as argument and the following new elements:

`par.clu`	`Integer matrix` with rows repersenting markers and columns corresponding to the parents. At a single marker position, parents with the same value were clustered in the same ancestral group.
`n.anc`	Average number of ancestral clusters along the genome.
`mono.anc`	Positions for which the ancestral clustering was monomorphic.

Author(s)

Vincent Garin

Examples

data(mppData_init)
data(par_clu)

mppData <- QC.mppData(mppData_init)
mppData <- IBS.mppData(mppData = mppData)

mppData <- IBD.mppData(mppData = mppData, type = 'RIL',
                       type.mating = 'selfing')
                       
mppData <- parent_cluster.mppData(mppData = mppData, par.clu  = par_clu)

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