QTL_R2 | R Documentation |
Computes the global and partial (adjusted) R squared of a list of QTLs using a linear model.
QTL_R2(mppData, trait = 1, QTL = NULL, Q.eff = "cr", glb.only = FALSE)
mppData |
An object of class |
trait |
|
QTL |
Object of class |
Q.eff |
|
glb.only |
|
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.
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. |
Vincent Garin
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.
QTL_select
, summary.QR2Res
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)
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