inc_mat_QTL {mppR}

QTL incidence matrix

Description

Build a single position QTL incidences matrix.

Usage

inc_mat_QTL(x, mppData, Q.eff, order.MAF = FALSE, ref_par = NULL)

Arguments

x

Integer value indicating the genetic position on the map (mppData$map) of the QTL incidence matrix.

mppData

An object of class mppData.

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. For more details see mpp_SIM. Default = "cr".

order.MAF

Logical value specifying if the QTL incidence matrix should be ordered by allele frequency for a parental and ancestral QTL incidence matrix. The colum will be ordred from the least to the most frequent allele. Default = FALSE.

ref_par

Optional Character expression defining the parental allele that will be used as reference for the parental model. Default = NULL

Value

Return:

QTL.mat

QTL incidence matrix. For the cross-specific model, it represents the difference between the number of allele from parent 2 or B and parent 1 or A divided by two. For parental (ancestral) model it represents the expected number of parental (ancestral) allele copies. For the bi-allelic model, it represents the number of copies of the least frequent allele.

Author(s)

Vincent Garin

Examples

data(mppData)

QTLmatCr <- inc_mat_QTL(x = 2, mppData = mppData, Q.eff = "cr")

QTLmatPar <- inc_mat_QTL(x = 2, mppData = mppData, Q.eff = "par")

QTLmatAnc <- inc_mat_QTL(x = 2, mppData = mppData, Q.eff = "anc")

QTLmatBi <- inc_mat_QTL(x = 2, mppData = mppData, Q.eff = "biall")