make_SFS: Generate a 1-2d site frequency spectrum from a dadi input...

In hemstrow/snpR: Whole-Genome Analysis Tools for Use with Single Nucleotide Polymorphism Data

Generate a 1-2d site frequency spectrum from a dadi input file.

Description

Generates a 1 or 2 dimensional site frequency spectrum from a dadi input file using the projection methods and folding methods of Marth et al (2004) and Gutenkunst et al (2009). This code is essentially an R re-implementation of the SFS construction methods implemented in the program dadi (see Gutenkunst et al (2009)).

Usage

make_SFS(x, pops, projection, fold = FALSE, update_bib = FALSE)

Arguments

x	character or data.frame. Either a path to a dadi formatted input file or a data.frame containing previously imported dadi formatted data.
pops	character. A vector of population names of up to length 2 containing the names of populations for which the an SFS is to be created.
projection	numeric. A vector of sample sizes to project the SFS to, in number of gene copies. Sizes too large will result in a SFS containing few or no SNPs.
fold	logical, default FALSE. Determines if the SFS should be folded or left polarized.
update_bib	character or FALSE, default FALSE. If a file path to an existing .bib library or to a valid path for a new one, will update or create a .bib file including any new citations for methods used. Useful given that this function does not return a snpRdata object, so a citations cannot be used to fetch references.

Details

Site frequency spectrums are constructed using the projection methods detailed in Marth et al (2004) and the 2 dimensional expansion in Gutenkunst et al (2009). Folding methods are also taken from Gutenkunst et al (2009). Either 1 or 2d SFSs can be constructed by providing a vector of population names and projection sizes.

Value

A matrix or vector containing the site frequency spectrum with a "pops" attribute containing population IDs, such as c("POP1", "POP2"). For a 2d SFS, the first pop is the matrix columns and the second is the matrix rows.

References

Gutenkunst et al (2009). Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS genetics, 5(10), e1000695.

Marth et al (2004). The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics, 166(1), 351-372.

hemstrow/snpR documentation built on March 20, 2024, 7:03 a.m.