qb.data {qtlbim} | R Documentation

## Prepares data for qb.mcmc

### Description

This function selects trait(s) and covariates from a `cross` object to build a model (`qb.model`) for MCMC (`qb.mcmc`).

### Usage

    qb.data( cross, pheno.col = 1, trait = c("normal","binary","ordinal"),
      fixcov = c(0), rancov = c(0), boxcox = FALSE, standardize = FALSE, ...)

### Arguments

`cross` | An object of class `cross`. See `read.cross` for details.
`pheno.col` | the column number for the phenotype used by `model`. Currently, only one phenotype can be analyzed at a time.
`trait` | Type of the quatitative trait or dependent variable: "normal" or "binary" or "ordinal".
`fixcov` | list of fixed covariates. The column number(s) in `cross$pheno` which is(are) considered as fixed covariates.
`rancov` | list of random covariates.The column number(s) in `cross$pheno` which is(are) considered as random covariates.
`boxcox` | Indicates whether to use a Boxcox transformation for the dependent variable or not: TRUE or FALSE. Note: trait has to be "normal" and all phenotypic values have to be positive for using this option.
`standardize` | Indicates whether to standardize the dependent variable or not: TRUE or FALSE. Note: trait has to be "normal" to use this option.
`...` | Extra terms not used.

### Details

This function picks the relevant part of the data from the `cross` object and prepares data for `qb.model` and `qb.mcmc` It can also standardize or transform continuous data if specified.

### Value

`yvalue` | vector of the values of the dependent variable.
`ncategory` | number of category type if it is non-normal data.
`envi` | environment effect: TRUE or FALSE.
`nfixcov` | number of fixed covariates.
`nrancov` | number of random covariates.
`fixcoef` | values of the fixed covariate(s) for all individuals.
`rancoef` | values of the random covariate(s) for all individuals.
`nran` | number of categories defining the random covariate.
`lamda` | value of lamda, the transformation parameter for the `boxcox` transformation.

### Note

This function returns a list and hence should have a differenct name from that of the `cross` object.

### Author(s)

Dr. Nengjun Yi, et al., nyi@ms.ssg.uab.edu

### References

http://www.qtlbim.org

### See Also

`qb.genoprob`, `qb.model`, `qb.mcmc`

### Examples

    qbData <- qb.data(cross, pheno.col = 3, rancov = 2, fixcov = 1)

[Package qtlbim version 1.6.5 Index]