QTL_R2 {mppR}

QTL global and partial R squared

Description

Computes the global and partial (adjusted) R squared of a list of QTLs using a linear model.

Usage

QTL_R2(mppData, trait = 1, QTL = NULL, Q.eff = "cr", glb.only = 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".

glb.only

Logical value. If glb.only = TRUE, only the global and global adjusted R squared will be returned. Default = FALSE.

Details

The function computes R squared statistics using a linear model. The extra variance explained by a full model containing the QTL terms with respect to a reduced model containing only the cross intercept terms and uses the ratio between the residual sum of square of these two models: R2 = 1-(RSS(f))/(RSS(r)).

Partial R squared for each individual QTL position can also be calculated. Two types of partial R squared are returned. The first one uses the difference between the R squared obtained with all QTL positions and the R squared obtain with all position minus the ith one (difference R squared). The second method used only the ith QTL position in the model (single R squared).

For both global and partial R squared, it is possible to obtained adjusted measurements taking the number of degrees of freedom into consideration using an adaptation of the formula given by Utz et al. (2000): R.adj = R-(z/(N-z-n.cr))*(1-R) where z is the total number of estimated components of the genetic effect. N is the total number of phenotypic information, and n.cr is the number of intercept (cross) terms.

Value

Return:

object of class QR2Res containing the following objects:

glb.R2

Global R squared of all QTL terms.

glb.adj.R2

Global adjusted R squared of all QTL terms.

part.R2.diff

Vector of partial R squared doing the difference between the full model and a model minus the ith QTL.

part.adj.R2.diff

Vector of partial adjusted R squared doing the difference between the full model and a model minus the ith QTL.

part.R2.sg

Vector of partial R squared using only the ith QTL.

part.adj.R2.sg

Vector of partial adjusted R squared using only the ith QTL.

Author(s)

Vincent Garin

References

Utz, H. F., Melchinger, A. E., & Schon, C. C. (2000). Bias and sampling error of the estimated proportion of genotypic variance explained by quantitative trait loci determined from experimental data in maize using cross validation and validation with independent samples. Genetics, 154(4), 1839-1849.

See Also

QTL_select, summary.QR2Res

Examples

data(mppData)

SIM <- mpp_SIM(mppData)
QTL <- QTL_select(Qprof = SIM, threshold = 3, window = 20)
Q_R2 <- QTL_R2(mppData = mppData, QTL = QTL, Q.eff = "cr")
summary(Q_R2)