mppGE_proc | R Documentation |
QTL detection in MPP characterized in multiple environments.
mppGE_proc( pop.name = "MPP", trait.name = "trait1", mppData, trait, EnvNames = NULL, VCOV = "UN", ref_par = NULL, VCOV_data = "unique", SIM_only = FALSE, thre.cof = 4, win.cof = 50, cof_red = FALSE, cof_pval_sign = 0.1, window = 20, thre.QTL = 4, win.QTL = 20, text.size = 18, n.cores = 1, maxIter = 100, msMaxIter = 100, verbose = TRUE, output.loc = NULL )
pop.name |
|
trait.name |
|
mppData |
An object of class |
trait |
|
EnvNames |
|
VCOV |
VCOV |
ref_par |
Optional |
VCOV_data |
|
SIM_only |
|
thre.cof |
|
win.cof |
|
cof_red |
|
cof_pval_sign |
|
window |
|
thre.QTL |
|
win.QTL |
|
text.size |
|
n.cores |
|
maxIter |
maximum number of iterations for the lme optimization algorithm. Default = 100. |
msMaxIter |
maximum number of iterations for the optimization step inside the lme optimization. Default = 100. |
verbose |
|
output.loc |
Path where a folder will be created to save the results. Default = NULL. |
The procedure is the following:
Simple interval mapping (SIM) to select cofactors
(mppGE_SIM
).
Composite interval mapping (CIM) with selected cofactors
(mppGE_CIM
).
Estimation of QTLs additive allelic effect
(QTL_effect_GE
).
Estimation of the global QTLs effect R squared and individual QTL effect
R squared (QTL_R2_GE
).
Return:
List containing the following items:
n.QTL |
Number of detected QTLs. |
cofactors |
|
QTL |
|
Q_eff |
|
R2 |
|
Some output files are also saved at the specified location
(output.loc
):
The SIM and CIM results in a RData file (SIM.RData, CIM.RData).
The list of cofactors (cofactors.RData).
The list of QTL (QTLs.RData).
The list of QTL allelic effects (QTL_effects.RData).
The QTL R squared statistics (QTL_R2.RData)
The number of detected QTLs and adjusted R2 (Glb_res.RData)
The plot of the CIM profile (QTL_profile.pdf) with dotted vertical
lines representing the cofactors positions and the
plot of the genetic effects per cross or parents obtained with
plot_allele_eff_GE
(gen_eff.pdf) with dashed
lines representing the QTL positions.
Vincent Garin
mppGE_CIM
,
mppGE_SIM
,
QTL_effect_GE
,
QTL_R2_GE
## Not run: data(mppData_GE) MPP_GE_QTL <- mppGE_proc(pop.name = 'EUNAM', trait.name = 'DMY', mppData = mppData_GE, trait = c('DMY_CIAM', 'DMY_TUM'), n.cores = 1, output.loc = tempdir()) ## End(Not run)
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