getprofile: Make a profile LOD score matrix for a given multiple QTL...
In ikwak2/funqtl: QTL Mapping for Function-Valued Traits

getprofile

R Documentation

Make a profile LOD score matrix for a given multiple QTL model.

Description

Calculate profile LOD scores for each chromosome.

Usage

getprofile(
  cross,
  pheno.cols,
  qtl,
  chr,
  pos,
  qtl.name,
  covar = NULL,
  formula,
  method = c("hk", "imp"),
  verbose = TRUE,
  tpy = c("comb", "sep")
)

Arguments

`cross`	An object of class `"cross"`. See `read.cross` for detail.
`pheno.cols`	Columns in the phenotype matrix to be used as the phenotype.
`qtl`	A QTL object, as produced by `makeqtl`, containing the positions of the QTL. Provide either `qtl` or the pair `chr` and `pos`.
`chr`	Vector indicating the chromosome for each QTL; if `qtl` is provided, this should not be.
`pos`	Vector indicating the positions for each QTL; if `qtl` is provided, this should not be.
`qtl.name`	Optional user-specified name for each QTL. If `qtl` is provided, this should not be.
`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.
`tpy`	type of output. If there are more QTL's in one chromosome. It plot them separately if `tpy = "sep"`, On the other hand, it combine then in one chromosome taking maximum values of them if `tpy = "comb"`.

Value

A "lodprofileM" or "lodprofileM2" object.

Author(s)

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

Examples

data(simspal)
simspal <- calc.genoprob(simspal, step=0)


phe <- 1:nphe(simspal)


# difference between tpy = "sep" and "comb"

par(mfrow=c(1,2))
qtlslod <- makeqtl(simspal, chr = c(1, 1, 4),
               pos = c(36.6, 61, 27.8), what = "prob")
lodmat1 <- getprofile(simspal, qtl =  qtlslod, pheno.cols =phe,
                    formula = y~Q1 + Q2 + Q3 , method = "hk", tpy = "sep")
plotprofile(lodmat1, main="tpy=\"sep\"")

lodmat2 <- getprofile(simspal, qtl =  qtlslod, pheno.cols =phe,
                    formula = y~Q1 + Q2 + Q3 , method = "hk", tpy = "comb")
plotprofile(lodmat2, main="tpy=\"comb\"")

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