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## Purpose: Test script for pedgene package
## Testing a simple 10-variant gene on both the X chrom and autosome
## Authors: Dan Schaid and Jason Sinnwell
## Created: 19-AUG-2013
## Updated: 11/7/2013
## alternatively:
require(kinship2)
require(pedgene)
data(example.ped)
data(example.geno)
data(example.map)
if(0) {
## delete above line to look at pedigrees
## quick look at the 3 pedigrees
pedall <- with(example.ped, pedigree(famid=ped, id=person, dadid=father,
momid=mother, sex=sex, affected=ifelse(is.na(trait), 0, trait)))
plot(pedall[1])
plot(pedall[2])
plot(pedall[3])
}
## simple tests of two genes (10 variants each)
## the genes are same variants, just on chroms 1 and X
pg.m2 <- pedgene(example.ped, example.geno, example.map, male.dose=2)
pg.m1 <- pedgene(example.ped, example.geno, example.map, male.dose=1)
## saved objects are of class pedgene, with items call (function call)
## and pgdf, a data.frame with a row for each gene
class(pg.m2)
names(pg.m2)
print(pg.m2, digits=4)
print(pg.m1, digits=4)
summary(pg.m2)
## Testing first gene with dose=2-dose
geno.recode <- cbind(example.geno[,1:2], 2-example.geno[,grep("AA", names(example.geno))])
pg.recode <- pedgene(example.ped, geno.recode, male.dose=2)
## note when map not given, assumes all 1 gene, and assigns "unknown" gene/chrom
pg.recode
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