make.analysis.obj {bqtl} | R Documentation |
Create commonly used objects for the analysis of a backcross or intercross experiment or of recombinant inbred lines.
make.analysis.obj(data, map.frame, marker.frame, marker.levels=NULL, method="F2", casewt=NULL,varcov=FALSE,mode.mat=NULL)
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:
NA's are allowed in marker.frame as well as the sixth
element("--" by default) to denote missing data. To use other
coding schemes replace "AA" and "aa" by codes for homozygous states,
"Aa" by the code for heterozygotes, "A-" by the code for 'not aa',
"a-" by the code for 'not AA', and "--" by the missing code.
Positions 3:5 are just placeholders if method!="F2" , but must
be present. | ||||||||||||||||||||||||||||
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:
method=="BC1" ( and the default marker.levels of
AA and Aa ),it is
marker.levels of
AA and aa ),it is
marker.levels will relabel the corresponding
rows.
|
A lot of stuff is bundled together in one object. The function is
really just a wrapper calling other make.*
functions.
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 |
This can be quite a LARGE object.It might be better in crosses with lots (say, thousands) of markers, or in which many 'virtual' markers are used, or on computers with limited RAM to store each component separately. Not all components are used in every type of analysis.
Charles C. Berry cberry@ucsd.edu
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
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 )