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DESCRIPTION
NAMESPACE
README.md
examples
rangeExpansion.Rproj

README.md

Range Expansion analysis

#################################################### this package serves as an example on how to analyze range expansion data, how to infer the origin and to infer the strength of the founder effect. Details of the methods are found in Peter & Slatkin (2013), Evolution and Peter & Slatkin (2015), Evolution

The major uses of the package are to either test isolation-by-distance on some sets of populations, or to infer the origin of an expansion, and possibly the strength of a founder effect.

The current version uses the snpStats package from Bioconductor to handle SNP data efficiently. See http://www.bioconductor.org/packages/release/bioc/html/snpStats.html on how to install it. In brief, you should be able to run

source("http://bioconductor.org/biocLite.R")
biocLite("snpStats")
library(snpStats)

Other dependencies are geosphere for haversine distance, and rworldmap for plotting of a map

Install

The easiest way to install the package is using devtools::install_github:

devtools::install_github("BenjaminPeter/rangeExpansion", ref="package")
library(rangeExpansion)

The example given here can then be run using

example(run.regions)

File Format Descriptions & Modifiers

there are two required files, one file contains genetic data and one containing location information.

The data formats are the following:

snp file (bed format)

see http://pngu.mgh.harvard.edu/~purcell/plink2/formats.html for reference. This file is perhaps easiest generated using plink 1.9. For example, from vcf data, use

plink --vcf my.vcf --set-missing-var-ids "@_#" --make-bed --out new --allow-extra-chr

to generate a bed file.

snp file (snapp format)

alternatively, data can be loaded using a similar format to the SNAPP program. Here, each row is an individual, each column (comma delimited) a SNP, except the first one, which gives the name of the individual. Missing data is encoded as a ?.

coords_file

a tab-delimited file with a header (first row) and the following columns:

  • id (or 1st column): is the id of the individual
  • longitude: the longitude or x-coordinate of sample location
  • latitude: the latitude or y-coordinate of the sample
  • outgroup (optional): Whether the individual should be treated as an outgroup to polarize SNP
  • region (optional): In the case of multiple origins, this allows for an factor for which individuals are included in a given run
  • pop (optional): If custom population assignments are chosen, the value here assigns individuals to a population

Pipeline Overview:

there are three main steps to this program:

  1. data is loaded from individuals, then population level data is generated from individual level data

  2. After that, a directionalit statistc is calculated for all pairs of populations, and a file with the location for each population is generated.

  3. These population matrices are used for the actual inference

Modelling decisions and options

Outgroups

Outgroup Individuals are individuals assumed to be ancestral to the population of interest. Their alleles can be used to determine the most likely ancestral state of an allele.

Regions

Regions are sets of populations that can be analyzed independently, i.e. they correspond to clusters that a priory are thought to have a different origin. Each list entry corresponds to an analysis, i. e. the following command will analyze the populations REGION_1, REGION_2 and REGION_3 individually, but will also jointly analyze REGION_1 and REGION_2. NULL corresponds to all individuals analyzed

regions_to_analyze <- list(NULL,
                           "REGION_1", 
                           "REGION_2", 
                           "REGION_3", 
                           c("REGION_1", "REGION_2"))

calculation of ψ

the script implents a basic pipeline from a genetic data set to a graphical output. If you are only interested in calculating the ψ statistic, use the get_psi function

the parameters for the function are: Parameters:
- fi : vector of int
- vector of derived allele counts for each snp in population i
- fj : vector of int
- vector of derived allele counts for each snp in population j
- ni : vector of int
- vector of total number of genotypes in
population i
- nj : vector of int
- vector of total number of genotypes in
population j
-n : the number of samples to downsample to
all vectors have length equal to the number of snp

Example analysis

Specify File Names

First, we need to specify the files we want to load

snp.file <- "examples/example_snp.snapp
coord.file <- "examples/example_coordinates.csv" 

We also need to specify the ploidy and which regions we want to analyze Suppose we want to analyze all individuals, and those which we assigned to individuals in "REGION_1", and "REGION_2":

ploidy <- 2 #diploid individuals
region <- list(NULL, 
               c("REGION_1", "REGION_2"))

Since the coordination file is csv, we add the argument sep=',':

raw.data <- load.data.snapp(snp.file, coord.file, sep=',', 
                            ploidy=ploidy)

Then, we calculate the population-level data from individual data and calculate all pairwise statistics:

pop <- make.pop(raw.data, ploidy)
psi <- get.all.psi(pop)

Finally, we want to find the origins, using run.regions:

results <- run.regions(region=region, pop=pop, xlen=10, ylen=20)

To analyze the results, we use the functions summary and plot:

summary gives a table with some statistcs, while plot gives a visual representation of the results

Summary Function

running the summary in the example should give a result like this:

     |         ALL|REGION_1+REGION_2

-------- |---------: | --------------: longitude| 125.5317| 136.0681 latitude | -16.41474| -13.02342 q |0.0006442162| 0.0005604015 r1 | 0.9987132| 0.9988805 r10 | 0.9872796| 0.9889162 r100 | 0.8858626| 0.8992156 d1 | 7.839768| 9.012298 rsq | 0.2742461| 0.08137551 pval |1.049256e-49| 0.2293561

  • longitude/latitude are the coordinates of the most likely origin
  • q is the strenght of the founder effect
  • r1/r10/r100 is the decrease in diversity over 1/10/100 km
  • rsq/pval are the correlation coefficient and correlation p-value for the most likely origin

Plot Function

The plot function gives a visual representation of the results. The arguments can be seen by typing ?plot.origin.results on the R console. In brief, a heatmap is generated where high (default: yellow) values indicate a likely origin (as measured by the sum of squares deviation), low values(red) indicate an unlikely origin and grey values indicate a negative correlation of diversity and an origin from that location. If add.map=T a map is added to the plot. The sample locations are added as circles, with colors measured as heterozygosities. Light circles indicate high H, dark circles indicate low H.

Example Output