GENOME-class: Class "GENOME"

Description Slots Methods Author(s) References Examples

Description

A class where all data and calculated values are stored

Slots

BIG.BIAL:

Biallelic matrix as an ff-object

SLIDE.POS:

Positions of biallelic sites (Sliding window mode)

big.data:

ff-package ?

gff.info:

Gff information ?

snp.data:

SNP data ?

basepath:

The basepath of the data

project:

—-

populations:

Populations definded before reading data

poppairs:

outgroup:

A vector of outgroup sequences

region.names:

Names/identifier of each region

feature.names:

Feature attributes of a given region

genelength:

Number of regions

keep.start.pos:

Start positions for sliding window

n.sites:

Total number of sites

n.sites2:

Total number of sites

n.biallelic.sites:

Number of biallelic sites (SNPs)

n.gaps:

Number of gaps observed in the data

n.unknowns:

Number of unknown.positions

n.valid.sites:

Sites without gaps

n.polyallelic.sites:

Sites with more than two variants

trans.transv.ratio:

Transition-transversion ratio

Coding.region:

Number of nucleotides in CDS regions

UTR.region:

Number of nucleotides in UTR regions

Intron.region:

Number of nucleotides in Intron regions

Exon.region:

Number of nucleotides in Exon regions

Gene.region:

Number of nucleotides in Gene regions

Pop_Neutrality:

Populations defined in the neutrality module

Pop_FSTN:

Populations defined in the FST (nucleotide) module

Pop_FSTH:

Populations defined in the FST (haplotype) module

Pop_Linkage:

Populations defined in the Linkage module

Pop_Slide:

Pop_MK:

Populations defined in the MK module

Pop_Detail:

Populations defined in the Detail module

Pop_Recomb:

Populations defined in the Recombination module

Pop_Sweeps:

Populations defined in the Selective sweeps module

FSTNLISTE:

nucleotide.F_ST:

Nucleotide FST

nucleotide.F_ST2:

nuc.diversity.between:

Nucleotide diversity between the populations

nuc.diversity.within:

Nucleotide diversity within the populations

nuc.F_ST.pairwise:

FST for each pair of populations

nuc.F_ST.vs.all:

FST for one population vs. all other individuals

n.haplotypes:

hap.diversity.within:

Haplotype diversity withing the populations

hap.diversity.between:

Haplotype diversity between the populations

Pi:

Pi from Nei

PIA_nei:

Pi between the populations

haplotype.counts:

Counts of the haplotypes observed

haplotype.F_ST:

Haplotype FST

hap.F_ST.pairwise:

Haplotype diversity for each pair of populations

Nei.G_ST.pairwise:

Haplotype diversity for each pair of populations

hap.F_ST.vs.all:

FST for one population vs. all other individuals

Nei.G_ST:

GST from Nei

Hudson.G_ST:

GST from Hudson

Hudson.H_ST:

HST from Hudson

Hudson.K_ST:

KST from Hudson

Hudson.Snn:

Snn from Hudson

Phi_ST:

Fixation index from Excoffier

hap.pair.F_ST:

MKT:

Mcdonald-Kreitman values

Tajima.D:

Tajima's D

SLIDE:

Fay.Wu.H:
Zeng.E:
theta_Tajima:
theta_Watterson:
theta_Fu.Li:
theta_Achaz.Watterson:
theta_Achaz.Tajima:
theta_Fay.Wu:
theta_Zeng:
Fu.Li.F:
Fu.Li.D:
Yach:
n.segregating.sites:

Total number of segregating sites

Rozas.R_2:
Fu.F_S:
Strobeck.S:
Kelly.Z_nS:
Rozas.ZZ:
Rozas.ZA:
Wall.B:
Wall.Q:
mult.Linkage:

Linkage disequilibrium between regions

RM:

Minimum number of recombination events (Hudson)

CL:

Composite likelihood of SNPs (Nielsen et. al)

CLmax:

Max. composite likelihood of SNPs (Nielsen et.al)

CLR:

Composite likelihood ratio test (Nielsen et. al)

MDSD:
MDG1:
MDG2:
genes:
region.data:

Detailed information about the data

region.stats:

Detailed (site-specific) statistics

D

Pattersons D statistic

f

the fraction of the genome that is admixed

jack.knife

jacknife mode

missing.freqs:

Missing nucleotide frequency

n.fixed.sites:

...

n.shared.sites:

...

n.monomorphic.sites:

...

BD:

...

BDF:

...

BDF_bayes:

...

alpha_ABBA:

...

alpha_BABA:

...

beta_BBAA:

...

Bd_clr:

...

Bd_dir:

...

D.pval:

...

D.z:

...

D.SE:

...

BDF.pval:

...

BDF.z:

...

BDF.SE:

...

P.Bd_clr:

...

RNDmin:

...

Methods

detail.stats

Several misc. statistics

diversity.stats

Haplotype and nucleotide diversities

diversity.between

Haplotype and nucleotide diversities

F_ST.stats.2

Snn from Hudson

F_ST.stats

Fixation index

getBayes

Get the input for BayeScanR

get.detail

Get the results from the Detail module

get.codons

Get information about the nature of codon changes

get.diversity

Get diversities from the FST module

get.F_ST

Get FST values from the FST module

get.linkage

Get the values from the Linkage module

get.MKT

Get Mcdonald-Kreitman values

getMS

get.neutrality

Get the values from the Neutrality module

get.status

Status of calculations

get.sum.data

Get some data observed from the alignments

linkage.stats

Linkage disequilibrium

calc.R2

Linkage disequilibrium

mult.linkage.stats

Linkage disequilibrium between regions

recomb.stats

Recombination statistics

sweeps.stats

Selective sweeps

Achaz.stats

Achaz's statistics

get.recomb

Get the values from the Recombination module

get.sweeps

Get the values frome the Selective Sweep module

set.ref.positions

Set the SNP positions

set.synnonsyn

Verify synonymous positions

splitting.data

Split the data into subsites

MKT

MKT Test

neutrality.stats

Neutrality statistics

popFSTN

Internal function

get.biallelic.matrix

Print the biallelic.matrix

set.populations

Define the populations

set.outgroup

Define the outgroup

get.individuals

get the names/IDs of individuals

region.as.fasta

Extract the region as a fasta file

show

show.slots

Show slots of the class GENOME

sliding.window.transform

Transform a GENOME object into a new object suitable for sliding window analysis

usage

PG_plot.biallelic.matrix

Plot the biallelic matrix

introgression.stats

Methods to measure archaic admixture

count.unknowns

Calculates the frequencies of missing nucleotides

calc.fixed.shared

Calculates the frequencies of missing nucleotides

set.filter

SNP Filtering

weighted.jackknife

weighted jackknife

Author(s)

Bastian Pfeifer

References

See the documentation for each module

Examples

1
2
3
#GENOME.class <- readData("Alignments")
#[email protected]
#[email protected]

Example output

Loading required package: ff
Loading required package: bit
Attaching package bit
package:bit (c) 2008-2012 Jens Oehlschlaegel (GPL-2)
creators: bit bitwhich
coercion: as.logical as.integer as.bit as.bitwhich which
operator: ! & | xor != ==
querying: print length any all min max range sum summary
bit access: length<- [ [<- [[ [[<-
for more help type ?bit

Attaching package: 'bit'

The following object is masked from 'package:base':

    xor

Attaching package ff
- getOption("fftempdir")=="/work/tmp/tmp/RtmpYTVRaU"

- getOption("ffextension")=="ff"

- getOption("ffdrop")==TRUE

- getOption("fffinonexit")==TRUE

- getOption("ffpagesize")==65536

- getOption("ffcaching")=="mmnoflush"  -- consider "ffeachflush" if your system stalls on large writes

- getOption("ffbatchbytes")==16777216 -- consider a different value for tuning your system

- getOption("ffmaxbytes")==536870912 -- consider a different value for tuning your system


Attaching package: 'ff'

The following objects are masked from 'package:bit':

    clone, clone.default, clone.list

The following objects are masked from 'package:utils':

    write.csv, write.csv2

The following objects are masked from 'package:base':

    is.factor, is.ordered

PopGenome documentation built on May 20, 2018, 5:03 p.m.