mpp_forward | R Documentation |
Multi-parent population QTL analysis model using a forward regression.
mpp_forward(
pop.name = "MPP",
trait.name = "trait1",
mppData,
trait = 1,
Q.eff = "cr",
ref.par = NULL,
sum_zero = FALSE,
threshold = 4,
window = 30,
backward = TRUE,
alpha.bk = 0.05,
plot.Qprof = FALSE,
plot.gen.eff = 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 |
|
ref.par |
Optional |
sum_zero |
Optional |
threshold |
|
window |
|
backward |
|
alpha.bk |
|
plot.Qprof |
|
plot.gen.eff |
|
CI |
|
drop |
|
text.size |
|
n.cores |
|
verbose |
|
output.loc |
Path where a folder will be created to save the results. By default the function uses the current working directory. |
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:
Forward regression to determine the a multi-QTL model. The function
selects successively QTL positions with -log10(pval) above the threshold.
Those positions are added as cofactors for following detection run.
The procedure stop when no more position has a -log10(pval) above the
threshold (QTL_forward
).
If backward = TRUE
, backward elimination on the final
list of detected QTLs.
Estimation of the QTL genetic effects and R squared statistics
(QTL_gen_effects
and QTL_R2
).
If CI = TRUE
, confidence interval calculation
based on a CIM- (composite interval mapping removing all cofactors on the
scanned chromosome) of the last run of the forward regression.
If plot.Qprof = TRUE
, plot of the last run of the forward
regression using plot.QTLprof
.
If plot.gen.eff = TRUE
, plot of the genetic effect distribution
along the genome of the last run of the forward regression using
plot.QTLprof
.
Return:
List containing the following items:
n.QTL |
Number of detected QTLs. |
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 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).
If plot.Qprof = TRUE
, the plot of the last regression run
(QTL_profile.pdf). 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_SIM
, plot.QTLprof
,
QTL_gen_effects
, QTL_forward
, QTL_R2
## Not run:
data(mppData)
# Specify a location where your results will be saved
my.loc <- "C:/.../..."
# Cross-specific model
USNAM_cr <- mpp_forward(pop.name = "USNAM", trait.name = "ULA",
mppData = mppData, plot.gen.eff = TRUE,
plot.Qprof = TRUE, CI = TRUE, output.loc = my.loc)
## End(Not run)
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