plot_allele_eff_GE {mppR}

plot of genome wide QTL allelic effect significance

Description

Plot of the genome wide significance of the QTL allelic effects in multiple environments.

Usage

plot_allele_eff_GE(
  mppData,
  nEnv,
  EnvNames,
  Qprof,
  Q.eff = "par",
  QTL = NULL,
  ref_par = NULL,
  main = "QTL genetic effects plot",
  text.size = 18
)

Arguments

mppData

An object of class mppData.

nEnv

Numeric number of environment or trait.

EnvNames

character expression indicating the environment or trait labels.

Qprof

object obtained with function mppGE_SIM, mppGE_CIM,

Q.eff

one of "cr", "par", "anc" or "biall". For the moment only "par" is available.

QTL

Optional argument. Object of class QTLlist representing a list of selected position obtained with the function QTL_select or a vector of character marker or in between marker positions names. These positions will be plotted on the graph. Default = NULL.

ref_par

Charater specifying the reference parent. Default = NULL.

main

Title of the graph. Default = "QTL genetic effects plot".

text.size

Numeric value specifying the size of graph axis text elements. Default = 18.

Author(s)

Vincent Garin

See Also

mppGE_CIM, mppGE_SIM

Examples

data(mppData_GE)

SIM <- mppGE_SIM(mppData = mppData_GE, trait = c('DMY_CIAM', 'DMY_TUM'))

Qpos <- QTL_select(Qprof = SIM, threshold = 3, window = 50)

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