mpp_back_elim: Backward elimination on QTL candidates

Description

Performs a backward elimination using a list of given QTLs positions. The positions with a p-value above the significance level alpha, are successively removed.

Usage

mpp_back_elim(mppData, trait = 1, QTL = NULL, Q.eff = "cr", alpha = 0.05)

Value

Return:

QTL: Data.frame of class QTLlist with five columns : 1) QTL marker names; 2) chromosomes; 3) interger position indicators on the chromosome; 4) positions in centi-Morgan; and 5) -log10(p-values).

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".
alpha: Numeric value indicating the level of significance for the backward elimination. Default = 0.05.

Author

Vincent Garin

Details

The function starts with all QTL positions in the model and test the inclusion of each position as the last in the model. If all position p-values are below alpha the procedure stop. If not the position with the highest p-value is remove and the procedure continue until there is no more unsignificant position.

Examples

Run this code


data(mppData)

SIM <- mpp_SIM(mppData)

QTL <- QTL_select(SIM)

QTL.sel <- mpp_back_elim(mppData = mppData, QTL = QTL)

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