GENOME-class: Class "GENOME"
In PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses

Description Slots Methods Author(s) References Examples

A class where all data and calculated values are stored

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:: ...
df:: ...
D3:: ...
Gmin:: ...
df_bayes:: ...
alpha_ABBA:: ...
alpha_BABA:: ...
beta_BBAA:: ...
Bd_clr:: ...
Bd_dir:: ...
D.pval:: ...
D.z:: ...
D.SE:: ...
df.pval:: ...
df.z:: ...
df.SE:: ...
P.Bd_clr:: ...
RNDmin:: ...

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

Bastian Pfeifer

See the documentation for each module

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#GENOME.class <- readData("Alignments")
#GENOME.class@n.sites
#GENOME.class@region.names

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