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 1.0-17 Index]