Haplin (version 3.5)

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://www.uib.no/smis/gjessing/genetics/software/haplin/

See Also

haplin, output

Examples

# Produce a table containing the most important output from haplin:
res <- haplin("data.dat", use.missing = T, maternal = T)
haptable(res)