refineqtlM: Refine the positions of QTL for function valued trait

In ikwak2/funqtl: QTL Mapping for Function-Valued Traits

Refine the positions of QTL for function valued trait

Description

Extended version of the R/qtl function refineqtl for function-valued traits. Iteratively scan the positions for QTL in the context of a multiple QTL model, to try to identify the positions that maximize "hk" and "f" criteria, for a fixed QTL model.

Usage

refineqtlM(
  cross,
  Y,
  qtl,
  formula,
  verbose = TRUE,
  maxit = 10,
  incl.markers = TRUE,
  keeplodprofile = TRUE,
  method = c("hk", "f", "sl", "ml"),
  pheno.cols
)

Arguments

cross	An object of class "cross". See read.cross for details.
Y	Matrix of phenotypes
qtl	A QTL object, as produced by makeqtl, containing the positions of the QTL.
formula	An object of class "formula" indicating the model to be fitted. (It can also be the character string representation of a formula.) QTLs are indicated as 'Q1', 'Q2', etc. Covariates are indicated by their names in covar.
verbose	If TRUE, give feedback about progress. If verbose is an integer > 1, further messages from scanqtl are also displayed.
maxit	Maximum number of iterations.
incl.markers	If FALSE, do calculations only at points on an evenly spaced grid.
keeplodprofile	If TRUE, keep the LOD profiles from the last iteration as attributes to the output.
method	Indicates whether to use "hk", "f", "sl", "ml" criteria
pheno.cols	Columns in the phenotype matrix to be used as the phenotype.

Details

This is an extended version of 'refineqtl' of 'qtl' package. For a multiple qtl model, this refines each qtl position to move for a better position that fits "hk" or "f" criteria given other qtl positions fixed. Do this process iteratively to find a refined version of multiple QTL.

Value

An object of class "qtl", with QTL placed in their new positions.

Author(s)

Il-Youp Kwak, <email: [e-mail]>

See Also

refineqtl, refineqtlM

Examples

cat("An example needs to be added.\n")

ikwak2/funqtl documentation built on April 20, 2022, 3:58 a.m.