mpp_proc | R Documentation |
Multi-parent population QTL analysis.
mpp_proc(
pop.name = "MPP",
trait.name = "trait1",
mppData,
trait = 1,
Q.eff = "cr",
plot.gen.eff = FALSE,
thre.cof = 3,
win.cof = 50,
N.cim = 1,
window = 20,
thre.QTL = 3,
win.QTL = 20,
backward = TRUE,
alpha.bk = 0.05,
ref.par = NULL,
sum_zero = FALSE,
CI = FALSE,
drop = 1.5,
text.size = 18,
n.cores = 1,
verbose = TRUE,
output.loc
)
pop.name |
|
trait.name |
|
mppData |
An object of class |
trait |
|
Q.eff |
|
plot.gen.eff |
|
thre.cof |
|
win.cof |
|
N.cim |
|
window |
|
thre.QTL |
|
win.QTL |
|
backward |
|
alpha.bk |
|
ref.par |
Optional |
sum_zero |
Optional |
CI |
|
drop |
|
text.size |
|
n.cores |
|
verbose |
|
output.loc |
Path where a folder will be created to save the results. |
The function run a full MPP QTL detection using models with different possible
assumptions concerning the number of alleles at the QTL position. For more
details about the different models, see documentation of the function
mpp_SIM
. The procedure is the following:
Simple interval mapping (SIM) to select cofactor
(mpp_SIM
).
Composite interval mapping (CIM) with selected cofactors
(mpp_CIM
).
Optional backward elimination on the list of QTL
candidates (backward = TRUE
) (mpp_back_elim
).
Computation of the QTL genetic effects (QTL_gen_effects
)
and proportion of the phenotypic variation explained by the QTLs (R squared)
(QTL_R2
).
Optional QTL confidence interval computation from a CIM- profile
(excluding cofactors on the scanned chromosome) (argument CI=TRUE
).
Return:
List containing the following items:
n.QTL |
Number of detected QTLs. |
cofactors |
|
QTL |
|
R2 |
|
QTL.effects |
|
QTL.CI |
If |
Some output files are also saved at the specified location
(output.loc
):
A QTL report (QTL_REPORT.txt) with: 1) the number of detected QTLs;
2) the global R squared statistics; 3) for each QTL, position information
(plus confidence interval if CI = TRUE
) and estimated QTL genetic
effects per cross or parents (for details see QTL_gen_effects
).
The SIM and CIM results in a text file (SIM.txt, CIM.txt).
The list of cofactors (cofactors.txt).
The list of QTL (QTL.txt).
The QTL R squared statistics (QTL_R2.txt) (for details see
QTL_R2
).
If CI = TRUE
, the QTL confidence intervals (QTL_CI.txt).
General results of the QTL detection process: number of QTLs and global adjusted and non-adjusted R squared statistics (QTL_genResults.txt).
The plot of the CIM profile (QTL_profile.pdf) with dotted vertical
lines representing the cofactors positions. If plot.gen.eff = TRUE
,
plot of the genetic effects per cross or parents (gen_eff.pdf) with dashed
lines representing the QTL positions. For more details see
plot.QTLprof
Vincent Garin
mpp_back_elim
,
mpp_CIM
,
mpp_perm
,
mpp_SIM
,
plot.QTLprof
,
QTL_gen_effects
,
QTL_R2
data(mppData)
# Specify a location where your results will be saved
my.loc <- tempdir()
# Cross-specific model
USNAM_cr <- mpp_proc(pop.name = "USNAM", trait.name = "ULA",
mppData = mppData, plot.gen.eff = TRUE, CI = TRUE,
verbose = FALSE, output.loc = my.loc)
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