haptable {Haplin}

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.

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.

Value

—- A dataframe is returned, with the following columns: —-

marker

Name(s) of marker(s) investigated

alleles

A listing of the alleles found at each marker

counts

Frequency counts of alleles at each marker

HWE.pv

P-value from Hardy-Weinberg equilibrium test at each marker

Original

Number of triads before removal

After.rem.NA

Number of triads after removal of missing

After.rem.Mend.inc.

Number of triads after removal of Mendelian inconsistencies

After.rem.unused.haplos

Number of triads after removal of unused (rare) haplotypes

pv.overall

Overall likelihood ratio p-value (test of all genetic effects combined)

haplos

Haplotypes (or single-marker alleles) found during estimation

haplofreq

Estimated haplotype frequencies

haplofreq.lower

Lower 95% CI for estimated haplotype frequencies

haplofreq.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 single dose relative risk

RR.upper

Upper 95% CI for single dose relative risk

RR.p.value

P-values for individual single dose effect

RRdd.est.

Estimated double dose relative risk

RRdd.lower

Lower 95% CI for double dose relative risk

RRdd.upper

Upper 95% CI for double dose relative risk

RRdd.p.value

P-values for individual double dose effect

NOTE1

When maternal = TRUE, there will be additional columns:

RRm.est.

Estimated single dose relative risk for maternal haplotype

RRm.lower

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

RRm.upper

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

RRm.p.value

P-values for individual single dose effect of maternal haplotype

RRmdd.est.

Estimated double dose relative risk for maternal haplotype

RRmdd.lower

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

RRmdd.upper

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

RRmdd.p.value

P-values for individual double dose effect of maternal haplotype

NOTE2

When poo = TRUE, the RR.est., RR.lower, and RR.upper columns will be replaced by the following columns:

RRcm.est.

Estimated single dose relative risk, when inherited from the mother

RRcm.lower

Lower 95% CI for single dose relative risk, when inherited from the mother

RRcm.upper

Upper 95% CI for single dose relative risk, when inherited from the mother

RRcm.p.value

P-values for individual single dose effects, when inherited from the mother

RRcf.est.

Estimated single dose relative risk, when inherited from the father

RRcf.lower

Lower 95% CI for single dose relative risk, when inherited from the father

RRcf.upper

Upper 95% CI for single dose relative risk, when inherited from the father

RRcf.p.value

P-values for individual single dose effects, when inherited from the father

RRcm_RRcf.est.

An estimate of parent-of-origin effect, i.e. the ratio RRcm/RRcf

RRcm_RRcf.lower

Lower 95% CI for ratio RRcm/RRcf

RRcm_RRcf.upper

Upper 95% CI for ratio RRcm/RRcf

RRcm_RRcf.p.value

P-value for parent-of-origin effect RRcm/RRcf at that marker

Note

Further information is found on the web page

Author(s)

Hakon K. Gjessing
Professor of Biostatistics
Division of Epidemiology
Norwegian Institute of Public Health
[e-mail]

References

Web Site: https://haplin.bitbucket.io

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)