mpp_back_elim {mppR} | R Documentation |
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)
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.
|
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.
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).
|
Author(s)
Vincent Garin
See Also
mpp_SIM
Examples
data(mppData)
SIM <- mpp_SIM(mppData)
QTL <- QTL_select(SIM)
QTL.sel <- mpp_back_elim(mppData = mppData, QTL = QTL)
[Package
mppR version 1.5.0
Index]