castedo / genomology

Genomic genealogy library in R

Genomic genealogy library in R

R code for analysis of family genome-wide DNA data (e.g. AncestryDNA and 23andme raw DNA data).

Visit the R homepage to learn more about the R statistical programming language. R is a popular system for doing professional DNA data analysis with Bioconductor packages.

This R package, genomology, is for doing genetic geneology and is a bit "hobby-ish" compared to what bioinformatics professionals would typically do with R and Bioconductor.

An example usage of this packge could be determining what percentage of genes a grand-child has received from grand-parents. This can be done with raw DNA data from AncestryDNA or 23andme for a grandparent, a "middle" parent and a grandchild.

Help

You can get package and function documentation from within R by doing:

library(genomology)
help(package="genomology")

Example

In this example:

• three family members DNA data is read (grandma, dad, girl) from different DNA services
• DNA data is merged together with extra information like genes and basepair ranges
• genotypes for lactase persistance (lactose tolerance) regulating gene MCM6 is printed
• estimation of which chromosome regions of girl are descended from grandma
• bar plot by chromosome of how much of girls DNA is inherited from dad's mom (grandma) vs dad's dad

library(genomology)
set.genomology.loci(read.csv("http://ref.castedo.com/dna/loci.csv", comment.char="#"))

grandma <- read.ancestrydna.web("http://example.com/dna-data-grandma.zip")
dad <- read.23andme.web("http://example.com/dna-data-dad.zip")
girl <- read.ancestrydna.web("http://example.com/dna-data-kid.zip")

dna <- grandma[, 1:3]
dna$zone <- chromozone(dna$chromosome, dna$position)
dna$gene <- locus.at(dna$chromosome, dna$position)
dna$gma <- grandma$genotype
dna$dad <- dad$genotype[match(dna$rsid, dad$rsid)]
dna$girl <- girl$genotype

dna <- dna[chromorder23(dna$chromosome, dna$position),]
dna$range <- chromorange(dna$chromosome, dna$position)

subset(dna, gene == 'LCT')

attach(dna)

kidNuc <- allele.assigned(assign.parent(dad, girl), girl)
dadMa <- assign.parent(gma, dad)
kidGrandSign <- assign.grandparents(dadMa, assign.passage(dad, kidNuc))
kidGrandSign[chromosome == 23] <- 1 # dad passes grandma's X to girl
gma.prob <- assign.descent(chromordinate(chromosome, position), kidGrandSign)

tab <- tapply(range/sum(range), list(call=prob.triage(gma.prob), zone=zone), sum)
tab[is.na(tab)] <- 0

barplot(tab, horiz=TRUE, las=1, ylab="Chromosome")

MATH

The core mathematical functions used in this package are idescent.prob and recombination.prob. Documentation is in the package help, but only the PDF (LaTeX) versions have the mathematical derivations. For convenience, the PDF versions are also online:

• idescent.prob
• recombination.prob

INSTALL

Clone this repository and from inside do

R CMD INSTALL package

Please email [email protected] if you install this package or want a built R package online (which would be easier to install).