mppGE_oneS_proc: MPP GxE one stage QTL analysis

In vincentgarin/mppGxE: MPP GxE QTL analysis

MPP GxE one stage QTL analysis

Description

One-stage QTL detection analysis in MPP characterized in multiple environments.

Usage

mppGE_oneS_proc(
  pop.name = "MPP",
  trait.name = "trait1",
  plot_data,
  mppData,
  trait,
  EnvNames = NULL,
  Q.eff = "cr",
  VCOV = "CS_CSRT",
  exp_des_form,
  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,
  verbose = TRUE,
  output.loc = NULL,
  workspace = 8e+06
)

Arguments

pop.name	Character name of the studied population. Default = "MPP".
trait.name	Character name of the studied trait. Default = "trait1".
plot_data	Data.frame containing the plot data with the following columns: the trait(s), 'genotype' (genotype indicator), 'check' (check indicator), 'cross' (cross indicator), 'env' (environment indicator), and all other experimental design covariates (e.g. replicate, blocks, etc.). The column names must be ('genotype', 'check', 'cross', env'). The names of the experimental design covariates must be the same as the one used in 'exp_des_form'. For more details see plot_data.
mppData	Object of class mppData contaning the the same genotype identifiers as the one in plot_data ('genotype').
trait	Character expression for the trait matching the trait column in 'plot_data' argument.
EnvNames	character expression indicating the environment or trait labels.
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: a) "CSRT" for within environment cross-specific residual terms; b) "CS_CSRT" for compound symmetry with within environment cross-specific residual terms. Default = "CS_CSRT".
exp_des_form	Character expression for the random experimental design effects in asreml-R format. For example, 'env:replicate + env:replicate:block'. The variable names used in 'exp_des_form' should strictly match the column names used in 'plot_data'.
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.
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.
workspace	Size of workspace for the REML routines measured in double precision words (groups of 8 bytes). The default is workspace = 8e6.

Details

The procedure is the following:

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

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

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

4. Optional estimation of QTLs additive allelic effect (mppGE_oneS_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.

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 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_oneS_CIM, mppGE_oneS_SIM, mppGE_oneS_back_elim, mppGE_oneS_QTL_effects plot_genEffects_GE,

Examples

## Not run: 

library(asreml)

data(mppData_GE)
data(plot_data)

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

QTL <- mppGE_oneS_proc(pop.name = 'EUNAM', trait.name = 'DMY',
                       plot_data = plot_data, mppData = mppData_GE,
                       trait = 'DMY', EnvNames = c('CIAM', 'TUM'),
                       Q.eff = 'par', exp_des_form = 'env:Rep + env:Rep:Block',
                       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.