Multiple imputation analysis for hap

Usage

mia(
  hapfile = "hap.out",
  assfile = "assign.out",
  miafile = "mia.out",
  so = 0,
  ns = 0,
  mi = 0,
  allsnps = 0,
  sas = 0
)

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.

Details

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.

It simply extracts outputs from hap.

Note

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

References

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

Clayton DG (2001) SNPHAP. https://github.com/chr1swallace/snphap.

Examples

if (FALSE) { # \dontrun{
# 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")
} # }