MQE_gen_effects {mppR}

QTL genetic effects multi-QTL effect model

Description

Compute a multi-QTL model with a list of QTL candidates (QTL) and return the decomposed QTL genetic effects per cross or per parents. The list of QTL can be of different types (cross-specific, parental, ancestral or bi-allelic). The type of QTL effects are specified in the vector Q.eff.

Usage

MQE_gen_effects(mppData = NULL, trait = 1, QTL = NULL, Q.eff, ref.par = NULL)

Arguments

mppData

An object of class mppData

trait

Numerical or character indicator to specify which trait of the mppData object should be used. Default = 1.

QTL

Vector of character markers positions names. Default = NULL.

Q.eff

Character vector indicating for each QTL position the type of QTL effect among: "cr", "par", "anc" and "biall". For details look at mpp_SIM.

ref.par

Optional Character expression defining the parental allele that will be used as reference for the parental model. For the ancestral model, the ancestral class containing the reference parent will be set as reference. This option can only be used if the MPP design is composed of a unique connected part. Default = NULL.

Details

This function computes for each QTL position the genetic effects of the cross, parental, ancestral or SNP allele components. For the cross-specific model (Q.eff = "cr"), the genetics effects represent the substitution effect of an single allele from the parent 2 (or B) with respect to an allele coming from the parent 1 or A. All effects are given in absolute value with the parent that cary the positive allele.

For the parental and the ancestral model (Q.eff = "par" or "anc"), the reference allele is defined per interconneted part. The most frequent parental (ancestral) allele is set as reference. Effects of the other alleles are estimated as deviation with respect to the reference. For more details about reference definition see QTL_gen_effects and design_connectivity.

For the bi-allelic model (Q.eff = "biall"), the genetic effects represent the effects of a single allele copy of the least frequent allele.

Value

Return:

results

List of data.frame (one per QTL) containing the following information:

1. QTL genetic effects per cross or parent.

2. Standard error of the QTL effects.

3. Test statistics of the effects (t-test or Wald statistic).

4. P-value of the test statistics.

5. Significance of the QTL effects.

6. For cross-specific model, parent with the positive additive effects.

7. For parental and ancestral model, indicator of connected part of the design and reference.

8. Allele scores of the parents if geno.par is non NULL in the mppData object.

Author(s)

Vincent Garin

See Also

MQE_proc, mpp_SIM, QTL_gen_effects, design_connectivity

Examples

data(mppData)

SIM <- mpp_SIM(mppData = mppData)
QTL <- QTL_select(SIM)

QTL.eff <- MQE_gen_effects(mppData = mppData, QTL = QTL[, 1],
                          Q.eff = c("anc", "par", "biall"))