pedigreeDeleteDuplicates: Remove duplicates from a pedigree

In GWASTools: Tools for Genome Wide Association Studies

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) 

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All row numbers refer to row in the full pedigree (not just within family). 
 Correct current problems and rerun pedigreeCheck.
There may be additional problems not investigated because of the current problems.

GWASTools documentation built on Nov. 8, 2020, 7:49 p.m.