gap (version 1.1-20)

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

Value

The returned value is a list containing:

Details

It simply extracts outputs from hap

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.

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")
# }