| mia {gap} | R Documentation |
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
mia(hapfile,assfile,miafile,so,ns,mi,allsnps,sas)
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 |
It simply extracts outputs from hap
The returned value is a list containing:
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
adapted from hap, in fact cline.c and cline.h are not used
## 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)