QTL_forward {mppR}

Forward regression QTL model

Description

Determines a multi-QTL model using a forward regression.

Usage

QTL_forward(
  mppData = NULL,
  trait = 1,
  Q.eff,
  threshold = 4,
  window = 30,
  n.cores = 1,
  verbose = TRUE
)

Arguments

mppData

An object of class mppData

trait

Numerical or character indicator to specify which trait of the mppData object should be used. Default = 1.

Q.eff

Character vector of possible QTL effects the user want to test. Elements of Q.eff can be "cr", "par", "anc" or "biall". For details look at mpp_SIM.

threshold

Numeric value representing the -log10(p-value) threshold above which a position can be considered as significant. Default = 4.

window

Numeric distance (cM) on the left and the right of a cofactor position where it is not included in the model. Default = 30.

n.cores

Numeric. Specify here the number of cores you like to use. Default = 1.

verbose

Logical value indicating if the steps of the forward regression should be printed. Default = TRUE.

Details

Forward regression to determine the a multi-QTL model. The function selects successively QTL positions with -log10(pval) above the threshold. Those positions are added as cofactors for following detection run. The procedure stop when no more position has a -log10(pval) above the threshold.

Value

Return:

QTL

Data.frame of class QTLlist with five columns : 1) QTL marker names; 2) chromosomes; 3) interger position indicators on the chromosome; 4) positions in centi-Morgan; and 5) -log10(p-values).

Author(s)

Vincent Garin

See Also

mpp_SIM,

Examples

data(mppData)

QTL <- QTL_forward(mppData = mppData, Q.eff = "par")