QTL_gen_effects {mppR}

QTL genetic effects

Description

Computes a multi-QTL model with a list of QTL candidates (QTL) and return the decomposed QTL effects per cross or per parents.

Usage

QTL_gen_effects(
  mppData,
  trait = 1,
  QTL = NULL,
  Q.eff = "cr",
  ref.par = NULL,
  sum_zero = FALSE
)

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

Object of class QTLlist representing a list of selected position obtained with the function QTL_select or vector of character marker positions names. Default = NULL.

Q.eff

Character expression indicating the assumption concerning the QTL effects: 1) "cr" for cross-specific; 2) "par" for parental; 3) "anc" for ancestral; 4) "biall" for a bi-allelic. For more details see mpp_SIM. Default = "cr".

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.

sum_zero

Optional Logical value specifying if the QTL effect of a parental or an ancestral model should be calculated using the sum to zero constraint. Default = FALSE.

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 carries the positive allele.

For the parental and the ancestral model (Q.eff = "par" or "anc"), it is possible to estimate maximum n-1 parental or ancestral alleles per interconnected part of the design. For these two models, one parental (ancestral) allele is set as reference per interconnected part of the design. Effects of the other alleles are estimated as deviation with respect to the reference. Connected parts of the design can be determined using Weeks and Williams (1964) method (design_connectivity). By default, the reference allele is the most frequent one. The user can also specify a parental allele that will be used as reference using the argument ref.par. This option is only available if the MPP design is composed of a unique connected part.

For the parental and ancestral model it is also possible to estimate the QTL effects using a sum to zero constraint sum_zero = TRUE. In that case, the effects of the different parental (ancestral) allele will represent the deviation with respect to the average trait value.

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:

Object of class QeffRes containing the following elements:

Qeff

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.

tab.Qeff

data.frame with one column per QTL giving the QTL genetic effects per cross or per parent with its significance. The first two rows indicate the chromosome and the position in cM of each QTL.

Author(s)

Vincent Garin

References

Weeks, D. L., & Williams, D. R. (1964). A note on the determination of connectedness in an N-way cross classification. Technometrics, 6(3), 319-324.

See Also

QTL_select, summary.QeffRes

Examples

data(mppData)

# QTL candidates

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

# Cross-specific model

QTL.effects <- QTL_gen_effects(mppData = mppData, QTL = QTL, Q.eff = "cr")
summary(QTL.effects)

# Parental model

QTL.effects <- QTL_gen_effects(mppData = mppData, QTL = QTL, Q.eff = "par")
summary(QTL.effects)

# Ancestral model

QTL.effects <- QTL_gen_effects(mppData = mppData, QTL = QTL, Q.eff = "anc")
summary(QTL.effects)

# Bi-allelic model

QTL.effects <- QTL_gen_effects(mppData = mppData, QTL = QTL, Q.eff = "biall")
summary(QTL.effects)