introgression.stats: Introgression statistics

Description Usage Arguments Details Value References Examples

Description

A generic function to estimate archaic admixture.

Usage

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## S4 method for signature 'GENOME'
introgression.stats(object,
subsites=FALSE,
do.D=FALSE,
do.BD=FALSE,
do.BDF=FALSE,
keep.site.info=TRUE,
block.size=FALSE,
dxy.table=FALSE,
D.global=FALSE,
do.CLR=FALSE,
dgt=2,
do.RNDmin=FALSE,
lambda=1)

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.BD

...

do.BDF

Bd-fraction

keep.site.info

Keep site specific values

block.size

jacknife

dxy.table

... not used ...

D.global

The global set of D,Bd values

do.CLR

Composite Likelihood approach

dgt

Digit for the CLR test

do.RNDmin

RNDmin (Rosenzweig, 2016)

lambda

Scale ... not used ...

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"

———————————————————
The following slots will be modified in the "GENOME" object
———————————————————

Slot Reference Description
1. D [1;eq. 2] Pattersons D statistic
2. f [2] f statistic
3. BDF [x] Bd-fraction
4. RNDmin [x] RNDmin

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

Examples

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# 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)
# GENOME.class <- introgression.stats(GENOME.class, do.BDF=TRUE)
# show the result:
# GENOME.class@D
# GENOME.class@f
# GENOME.class@BDF

PopGenome documentation built on May 29, 2017, 9:11 p.m.

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