introgression.stats: Introgression statistics

In pievos101/PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Introgression statistics

Description

A generic function to estimate archaic admixture.

Usage

## S4 method for signature 'GENOME'
introgression.stats(object,
subsites=FALSE,
do.D=TRUE,
do.df=TRUE,
keep.site.info=TRUE,
block.size=FALSE,
do.RNDmin=FALSE,
l.smooth=FALSE)

Arguments

object	An object of class "GENOME"
subsites	"transitions": SNPs that are transitions. "transversions": SNPs that are transversions. "syn": synonymous sites. "nonsyn": nonsynonymous sites. "exon": SNPs in exon regions. "intron": SNPs in intron regions. "coding": SNPs in coding regions (CDS). "utr": SNPs in UTR regions. "gene": SNPs in genes. "intergenic" : SNPs in intergenic regions.
do.D	Pattersons D and Martin's f statistic
do.df	d-fraction
keep.site.info	keep site specific values ([e-mail])
block.size	the block size for jackknife
do.RNDmin	RNDmin (Rosenzweig, 2016)
l.smooth	laplace smoothing for Bd-fraction

Details

To perform the D and f statistic one needs to define 3 populations via the function set.populations,
where the third population represent the archaic population. In addition, an outgroup is required and have to be set via the function set.outgroup. Here, only SNPs where the outgroup is monomorphic are considered. f is the fraction of the genome that is admixed [2].

Value

Returned value is a modified object of class "GENOME"

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The following slots will be modified in the "GENOME" object
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	Slot	Reference	Description
1.	D	[1;eq. 2]	Pattersons D statistic
2.	f	[2]	f statistic
3.	df	[3]	Bd-fraction
4.	RNDmin	[x]	RNDmin
5.	D.z	[x]	z values (jackknife)
6.	D.pval	[x]	P values (jackknife)
7.	df.z	[3]	z values (jackknife)
8.	df.pval	[3]	P values (jackknife)

References

[1] Durand, E. Y., Patterson, N. J., Reich, D., & Slatkin, M. (2011). Testing for ancient admixture between closely related populations.
Molecular Biology and Evolution, 28(8), 2239–2252. doi:10.1093/molbev/msr048
[2] Simon H Martin, Kanchon K Dasmahapatra, Nicola J Nadeau, et al. (2013). Genome-wide evidence for speciation with gene flow in Heliconius butterflies.
Genome Res. doi:10.1101/gr.159426.113
[3] Bastian Pfeifer and Durrell D. Kapan (2019). Estimates of introgression as a function of pairwise distances.
BMC Bioinformatics. https://doi.org/10.1186/s12859-019-2747-z

Examples

# GENOME.class <- readData("\home\Alignments")
# GENOME.class <- set.populations(GENOME.class,list(1:3,4:8,9:12))
# GENOME.class <- set.outgroup(GENOME.class,13)
# GENOME.class <- introgression.stats(GENOME.class, do.D=TRUE)
# show the result:
# GENOME.class@D
# GENOME.class@f
# GENOME.class <- introgression.stats(GENOME.class, do.df=TRUE)
# show the result:
# GENOME.class@df

pievos101/PopGenome documentation built on Feb. 24, 2023, 7:11 a.m.