bqtl (version 1.0-7)

make.analysis.obj: Set up data for QTL mapping

Description

Create commonly used objects for the analysis of a backcross or intercross experiment or of recombinant inbred lines.

Usage

make.analysis.obj(data, map.frame, marker.frame, marker.levels=NULL,
method="F2", casewt=NULL,varcov=FALSE,mode.mat=NULL)

Arguments

data

A data.frame (or vector) of phenotype and (optionally) covariate information

map.frame

A map.frame.object (see make.map.frame) encoding the map information and other details of the study

marker.frame

A marker.frame.object. A matrix or data.frame of marker state information.

marker.levels

A vector of length six or NULL. If NULL then the defaults for the elements are:

lccc{ Element F2.default BC.default RI.default 1 "AA" "AA" "AA"

method

One of "F2", "BC1", "RI.self", or "RI.sib"

casewt

If there are multiple observations on one genotype (such as in recombinant inbreds) this can be used to assign a weight to each observation. The wisdom of doing this is debatable.

varcov

If FALSE, don't create a varcov.object. Otherwise give an index into data to select a dependent variable. See varcov

mode.mat

If NULL use the default. For method=="F2" ( and the default marker.levels of AA, Aa, and aa ), this is a 3 by 2 matrix: lrr{ Genotype add

Value

• A list with components
• data
  data.frame of phenotype, covariate information, and regressors created by make.regressor.matrix
• varcov
  A varcov.object. See make.varcov
• reg.names
  The names of the regressors from make.regressor.matrix
• method
  The method argument in the call.
• state.matrix
  See make.state.matrix
• loc.right
  See make.loc.right
• map.frame
  See make.map.frame
• casewt
  The casewt argument
• mode.mat
  The mode.mat used
• version
  A string giving the version of BQTL from qhich the objects was created
• call
  The function call

Details

A lot of stuff is bundled together in one object. The function is really just a wrapper calling other make.* functions.

See Also

make.map.frame for definition of the marker map, The internally used functions are: make.loc.right, make.state.matrix, make.regressor.matrix, make.varcov, and make.marker.numeric

Examples

data( little.bc.pheno )
data( little.mf.5 )
data( little.bc.markers )
names(little.bc.pheno)
little.ana.bc <- make.analysis.obj(little.bc.pheno$bc.phenotype,
                                   little.mf.5,little.bc.markers,
                                   method="BC1")
summary( little.ana.bc )

<testonly>rm( little.ana.bc, little.bc.pheno, little.mf.5, little.bc.markers )</testonly>