pedigreeDeleteDuplicates: Remove duplicates from a pedigree

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

Remove duplicates from a pedigree

Description

pedigreeDeleteDuplicates removes duplicates from a pedigree.

Usage

pedigreeDeleteDuplicates(pedigree, duplicates)

Arguments

pedigree	A dataframe containing the pedigree information for the samples to be examined with columns labeled "family", "individ", "mother", "father" and "sex" containing the identifiers of the family, individual, individual's mother, individual's father and individual's sex (coded as "M" or "F") .
duplicates	dataframe with columns "family" (family id) and "individ" (individual id).

Details

The output of pedigreeCheck can be provided to pedigreeDeleteDuplicates in order to generate a new pedigree with duplicates removed.

Value

The output of pedigreeDeleteDuplicates is a pedigree identical to pedigree, but with duplicates removed.

Author(s)

Cecelia Laurie

See Also

pedigreeCheck, pedigreePairwiseRelatedness

Examples

family <- c(1,1,1,1,2,2,2,2)
individ <- c(1,2,3,3,4,5,6,6)
mother <- c(0,0,1,1,0,0,4,4)
father <- c(0,0,2,2,0,0,5,5)
sex <- c("F","M","F","F","F","F","M","M")
pedigree <- data.frame(family, individ, mother, father, sex, stringsAsFactors=FALSE)
duplicates <- pedigreeCheck(pedigree)$duplicates
pedigree.no.dups <- pedigreeDeleteDuplicates(pedigree, duplicates) 

smgogarten/GWASTools documentation built on July 4, 2023, 2:32 a.m.