haptable: Create haplin table

In Haplin: Analyzing Case-Parent Triad and/or Case-Control Data with SNP Haplotypes

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)

Haplin documentation built on Sept. 11, 2024, 7:13 p.m.