tdt.plink: Perform family-based transmission diseqiulibrium test (TDT)...

In andrewparkermorgan/argyle: Basic interface and QC for genotypes from Illumina Infinium arrays

Description

Perform family-based transmission diseqiulibrium test (TDT) with PLINK

Usage

tdt.plink(prefix, perms = FALSE, geno.missing = 0, ind.missing = 0,
  maf = 0, hwe = 1,
  flags = "--keep-allele-order --allow-no-sex --nonfounders", ...)

Arguments

prefix	a pointer to a PLINK fileset (of class plink)
perms	logical: establish significance thresholds using adaptive permutation, or skip it?
geno.missing	drop markers with call rate lower than this threshold
ind.missing	drop samples with call rate lower than this threshold
maf	drop markers with minor-allele frequency lower than this threhsold
hwe	drop markers p-value less than this threshold for test of Hardy-Weinbery equilibrium
flags	additional command-line flags passed directly to PLINK call
...	ignored

Details

Requires a case-control phenotype. See the relevant PLINK documentation for details of the underlying calculations.

Value

a dataframe with association results, having the following columns:

• chr

• pos

• marker

• A1 – reference allele (interpretation depends on dataset)

• p.value – p-value for hypothesis test

• OR – odds ratio (in case-control context)

• n – count of non-missing genotypes at this marker

• test – which family of hypothesis test this is

• p.value.perm – empirical p-value from permutations, if applicable

References

PLINK v1.9: https://www.cog-genomics.org/plink2

Purcell S et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81(3): 559-575. doi:10.1086/519795.

andrewparkermorgan/argyle documentation built on May 10, 2019, 11:08 a.m.