Haplin (version 6.0.1)

haptable: Create haplin table

Description

Create a comprehensive table of haplin output

Usage

haptable(object)

Arguments

object

A haplin object, i.e. the result of running haplin.

Value

A dataframe is returned, with the following columns:

Original

Number of triads

After.rem.NA

Number of triads after removal of missing

After.rem.Mend..inc.

Number of triads after removal of Mendelian inconsistencies

After.rem.rare.haplos

Number of triads after removal of rare haplotypes

alleles

Alleles at each SNP

counts

Frequency counts for alleles

HWE.pv

P-value for deviation from HWE

haplo

Haplotypes found during estimation

pv.overall

Overall p-value

hfreq.est.

Estimated haplotype frequencies

hfreq.lower

Lower 95% CI for estimated haplotype frequencies

hfreq.upper

Upper 95% CI for estimated haplotype frequencies

reference

Reference method. If ref.cat is used, the reference category is labeled "ref"

RR.est.

Estimated single dose relative risk

RR.lower

Lower 95% CI for estimated single dose relative risk

RR.upper

Upper 95% CI for estimated single dose relative risk

RR.p.value

P-values for individual single dose estimates

RRdd.est.

Estimated double dose relative risk

RRdd.lower

Lower 95% CI for estimated double dose relative risk

RRdd.upper

Upper 95% CI for estimated double dose relative risk

RRdd.p.value

P-values for individual double dose estimates

RRm.est.

Estimated single dose relative risk for maternal haplotype

RRm.lower

Lower 95% CI for estimated single dose relative risk for maternal haplotype

RRm.upper

Upper 95% CI for estimated single dose relative risk for maternal haplotype

RRm.p.value

P-values for individual single dose estimates for maternal haplotype

RRmdd.est.

Estimated double dose relative risk for maternal haplotype

RRmdd.lower

Lower 95% CI for estimated double dose relative risk for maternal haplotype

RRmdd.upper

Upper 95% CI for estimated double dose relative risk for maternal haplotype

RRmdd.p.value

P-values for individual double dose estimates for maternal haplotype

Note that the results from the maternal haplotype risks will not be present unless maternal = T was used in the haplin call.

Details

haptable extracts the most important information from a haplin object to produce a summary table. The table can then be saved with, for instance, write.table, making the results easily accessible to other applications. You can also use output to produce and save the same results.

References

Web Site: http://folk.uib.no/gjessing/genetics/software/haplin/

See Also

haplin, output

Examples

## Not run: 
# 
# # Produce a table containing the most important output from haplin:
# res <- haplin("data.dat", use.missing = T, maternal = T)
# haptable(res)
# 
# 
# 
# ## End(Not run)