refineqtlF: Refine the positions of QTL for function valued trait
In ikwak2/funqtl: QTL Mapping for Function-Valued Traits

refineqtlF

R Documentation

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 SLOD criteria, for a fixed QTL model.

Usage

refineqtlF(
  cross,
  pheno.cols,
  usec = c("slod", "mlod"),
  qtl,
  covar = NULL,
  formula,
  method = c("hk", "imp"),
  verbose = TRUE,
  maxit = 10,
  incl.markers = TRUE,
  keeplodprofile = TRUE
)

Arguments

`cross`	An object of class `"cross"`. See `read.cross` for details.
`pheno.cols`	Columns in the phenotype matrix to be used as the phenotype.
`usec`	Which method to use (`"slod"` or `"mlod"`)
`qtl`	A QTL object, as produced by `makeqtl`, containing the positions of the QTL.
`covar`	A matrix or data.frame of covariates. These must be strictly numeric.
`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`.
`method`	Indicates whether to use multiple imputation or Haley-Knott regression.
`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.

Value

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

Author(s)

Il-Youp Kwak, <email: ikwak2@stat.wisc.edu>

References

Zeng, Z.-B., Kao, C.-H., and Basten, C. J. (1999) Estimating the genetic architecture of quantitative traits. _Genet. Res._ *74*, 279-289.

Haley, C. S. and Knott, S. A. (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. _Heredity_ *69*, 315-324.

Examples

data(exd)
exd <- calc.genoprob(exd, step=2)
qtl1.c <- makeqtl(exd, chr = 2, pos = 30, what = "prob")
thisqtl1.c <- refineqtlF(exd, pheno.cols = 1:10,  qtl = qtl1.c,
                         method = "hk")

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