mppGE_oneS_CIM: MPP GxE one stage CIM analysis

In vincentgarin/mppGxE: MPP GxE QTL analysis

MPP GxE one stage CIM analysis

Description

Perform a MPP GxE one stage CIM analysis.

Usage

mppGE_oneS_CIM(
  plot_data,
  mppData,
  trait,
  Q.eff = "cr",
  VCOV = "CS_CSRT",
  exp_des_form,
  cofactors = NULL,
  window = 20,
  plot.gen.eff = FALSE,
  workspace = 8e+06
)

Arguments

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.
Q.eff	Character expression indicating the assumption concerning the QTL effects: 1) "cr" for cross-specific; 2) "par" for parental; 3) "anc" for ancestral; 4) "biall" for a bi-allelic. 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'.
cofactors	Object of class QTLlist representing a list of selected marker positions obtained with the function QTL_select() or a vector of character marker positions names. Default = NULL.
window	Numeric distance (cM) on the left and the right of a cofactor position where it is not included in the model. Default = 20.
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.
workspace	Size of workspace for the REML routines measured in double precision words (groups of 8 bytes). The default is workspace = 8e6.

Value

Return:

CIM	Data.frame of class QTLprof. with five columns : 1) QTL marker or in between position names; 2) chromosomes; 3) interger position indicators on the chromosome; 4) positions in centi-Morgan; and 5) -log10(p-val). And if plot.gen.eff = TRUE, p-values of the cross or parental QTL allelic effects.

Author(s)

Vincent Garin

See Also

plot_genEffects_GE

Examples

## Not run: 

library(asreml)

data(mppData_GE)
data(plot_data)


cofactors <- c("PZE.105068880", "PZE.106098900")

# takes 10 min

CIM <- mppGE_oneS_CIM(plot_data = plot_data, mppData = mppData_GE,
                      trait = 'DMY', Q.eff = 'par',
                      exp_des_form = 'env:Rep + env:Rep:Block',
                      cofactors = cofactors, plot.gen.eff = TRUE)

plot(x = CIM)

plot_genEffects_GE(mppData = mppData_GE, nEnv = 2, EnvNames = c('CIAM', 'TUM'),
                   Qprof = CIM, Q.eff = 'par', QTL = Qpos, text.size = 14)



## End(Not run)

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