mppGE_proc: MPP GxE QTL analysis

In vincentgarin/mppGxE: MPP GxE QTL analysis

MPP GxE QTL analysis

Description

QTL detection in MPP characterized in multiple environments.

Usage

mppGE_proc(
  pop.name = "MPP",
  trait.name = "trait1",
  mppData,
  trait,
  EnvNames = NULL,
  Q.eff = "cr",
  VCOV = "CS_CSRT",
  plot.gen.eff = FALSE,
  thre.cof = 4,
  win.cof = 50,
  N.cim = 1,
  window = 20,
  thre.QTL = 4,
  win.QTL = 20,
  alpha = 0.01,
  Qeff_est = TRUE,
  text.size = 18,
  parallel = FALSE,
  cluster = NULL,
  workspace = 8e+06,
  verbose = TRUE,
  output.loc = NULL
)

Arguments

pop.name	Character name of the studied population. Default = "MPP".
trait.name	Character name of the studied trait. Default = "trait1".
mppData	An object of class mppData.
trait	Character vector specifying which traits (environments) should be used.
EnvNames	character expression indicating the environment or trait labels. By default: Env_1, 2, 3, etc.
Q.eff	Character expression indicating the assumption concerning the QTL effect: 1) "cr" for cross-specific effects; 2) "par" parental effects; 3) "anc" for an ancestral effects; 4) "biall" for a bi-allelic effects. Default = "cr".
VCOV	VCOV Character expression defining the type of variance covariance structure used. "ID" for identity, "CSRT" for within environment cross-specific residual terms, "CS_CSRT" for compound symmetry with within environment cross-specific residual terms. Default = "CS_CSRT".
plot.gen.eff	Logical value. If plot.gen.eff = TRUE, the function will save the significance of the QTL allelic effects per cross/parent along the genome. These results can be visualized with the function plot_genEffects_GE. Default value = FALSE.
thre.cof	Numeric value representing the -log10(p-value) threshold above which a position can be selected as cofactor. Default = 4.
win.cof	Numeric value in centi-Morgan representing the minimum distance between two selected cofactors. Default = 50 cM.
N.cim	Numeric value specifying the number of times the CIM analysis is repeated. Default = 1.
window	Numeric distance (cM) on the left and the right of a cofactor position where it is not included in the model. Default = 20.
thre.QTL	Numeric value representing the -log10(p-value) threshold above which a position can be selected as QTL. Default = 4.
win.QTL	Numeric value in centi-Morgan representing the minimum distance between two selected QTLs. Default = 20.
alpha	Numeric value indicating the level of significance for the backward elimination. Default = 0.01.
Qeff_est	Logical value specifying if the QTL effects of the final QTL list should be estimated. Default = TRUE.
text.size	Numeric value specifying the size of graph axis text elements. Default = 18.
parallel	Logical value specifying if the function should be executed in parallel on multiple cores. To run the function in parallel user must provide clusters in the cluster argument. Parallelization is only available for 'ID' model. Default = FALSE.
cluster	Cluster object obtained with the function makeCluster() from the parallel package. Default = NULL.
workspace	Size of workspace for the REML routines measured in double precision words (groups of 8 bytes). The default is workspace = 8e6.
verbose	Logical value indicating if the steps of mpp_proc should be printed. It will not affect the printing of the other functions called by mpp_proc(), especially the printing of asreml(). Default = TRUE.
output.loc	Path where a folder will be created to save the results. Default = NULL.

Details

The procedure is the following:

1. Simple interval mapping (SIM) to select cofactor (mppGE_SIM).

2. Composite interval mapping (CIM) with selected cofactors (mppGE_CIM).

3. Backward elimination on the list of QTLs (mppGE_back_elim).

4. Optional estimation of QTLs additive allelic effect (mppGE_QTL_effects).

Value

Return:

List containing the following items:

n.QTL	Number of detected QTLs.
cofactors	Data.frame with cofactors positions.
QTL	Data.frame with QTL positions.
R2	List containing R squared statistics of the QTL effects. For details see QTL_R2 output section.

Some output files are also saved at the specified location (output.loc):

1. The SIM and CIM results in a text file (SIM.txt, CIM.txt).

2. The list of cofactors (cofactors.txt).

3. The list of QTL (QTL.txt).

4. The QTL R squared statistics (QTL_R2.txt) (for details see QTL_R2).

5. 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 obtained with plot_genEffects_GE (gen_eff.pdf) with dashed lines representing the QTL positions.

Author(s)

Vincent Garin

See Also

mppGE_CIM, mppGE_SIM, mppGE_back_elim, mppGE_QTL_effects, plot_genEffects_GE

Examples

## Not run: 

library(asreml)

data(mppData_GE)

# Specify a location where your results will be saved
my.loc <- tempdir()

QTL <- mppGE_proc(pop.name = 'EUNAM', trait.name = 'DMY', mppData = mppData_GE,
                  trait = c('DMY_CIAM', 'DMY_TUM'), EnvNames = c('CIAM', 'TUM'),
                  Q.eff = 'par', plot.gen.eff = TRUE, thre.cof = 3,
                  thre.QTL = 3, verbose = FALSE, output.loc = my.loc)


## End(Not run)

vincentgarin/mppGxE documentation built on June 25, 2022, 2:45 p.m.