plot_allele_eff_GE: plot of genome wide QTL allelic effect significance

In vincentgarin/mppR: Multi-Parent Population QTL Analysis

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)

vincentgarin/mppR documentation built on March 13, 2024, 7:30 p.m.