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mia

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

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)

gap

Genetic Analysis Package

v1.2.3-1

GPL (>= 2)

Authors

Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley

Initial release

2021-4-21

mia