pedigreeDeleteDuplicates removes duplicates
from a 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") .
dataframe with columns "family" (family id) and "individ" (individual id).
The output of
pedigreeCheck can be provided
pedigreeDeleteDuplicates in order to generate a new
pedigree with duplicates removed.
The output of
pedigreeDeleteDuplicates is a pedigree
pedigree, but with duplicates removed.
1 2 3 4 5 6 7 8
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)
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.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.