R: multiple imputation analysis for hap

mia {gap} | R Documentation

## multiple imputation analysis for hap

### Description

This command reads outputs from hap session that uses multiple imputations, i.e. -mi\# option. To simplify matters it assumes -ss option is specified together with -mi option there.

This is a very naive version of MIANALYZE, but can produce results for PROC MIANALYZE of SAS

### Usage

    mia(hapfile,assfile,miafile,so,ns,mi,allsnps,sas)

### Arguments

`hapfile` | hap haplotype output file name
`assfile` | hap assignment output file name
`miafile` | mia output file name
`so` | to generate results according to subject order
`ns` | do not sort in subject order
`mi` | number of multiple imputations used in hap
`allsnps` | all loci are SNPs
`sas` | produce SAS data step program

### Details

It simply extracts outputs from hap

### Value

The returned value is a list containing:

### References

Zhao JH and W Qian (2003) Association analysis of unrelated individuals using polymorphic genetic markers. RSS 2003, Hassalt, Belgium

Clayton DG (2001) SNPHAP. http://www-gene.cimr.cam.ac.uk/clayton/software.

### Note

adapted from hap, in fact cline.c and cline.h are not used

### See Also

`hap`

### Examples

    ## Not run:
    # 4 SNP example, to generate hap.out and assign.out alone
    data(fsnps)
    hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4)

    # to generate results of imputations
    control <- hap.control(ss=1,mi=5)
    hap(id=fsnps[,1],data=fsnps[,3:10],nloci=4,control=control)

    # to extract information from the second run above
    mia(so=1,ns=1,mi=5)
    file.show("mia.out")

    ## commands to check out where the output files are as follows:
    ## Windows
    # system("command.com")
    ## Unix
    # system("csh")

    ## End(Not run)

[Package gap version 1.2.1 Index]