edit.loci
(Package: pegas) :
Edit Allelic Data with R's Data Editor
This allows to edit a data frame of class "loci" with R's spreadsheet-like data editor.
● Data Source:
CranContrib
● Keywords: IO
● Alias: edit.loci
●
0 images
|
R2.test
(Package: pegas) :
Ramos-Onsins--Rozas Test of Neutrality
This function computes Ramos-Onsins and Rozas's test of neutrality for a set of DNA sequences.
● Data Source:
CranContrib
● Keywords: htest
● Alias: R2.test
●
0 images
|
diffHaplo
(Package: pegas) :
Comparison Between Two Haplotypes
This function compares two haplotypes and returns a summary of the differences.
● Data Source:
CranContrib
● Keywords: manip
● Alias: diffHaplo
●
0 images
|
LD
(Package: pegas) :
Linkage Disequilibrium
These two functions analyse linkage disequilibrium in the case of phased (LD) or unphased (LD2) genotypes.
● Data Source:
CranContrib
● Keywords: models
● Alias: LD, LD2
●
0 images
|
alleles2loci
(Package: pegas) :
Build Loci Object From Matrix of Alleles
This function transforms a matrix of alleles into an object of class "loci".
● Data Source:
CranContrib
● Keywords: IO
● Alias: alleles2loci
●
0 images
|
haplotype.loci
(Package: pegas) :
Haplotype Extraction and Frequencies From Allelic Data
This function extracts haplotypes from phased genotypes.
● Data Source:
CranContrib
● Keywords: manip
● Alias: dist.haplotype.loci, haplotype.loci, plot.haplotype.loci
●
0 images
|
utilities
(Package: pegas) :
Utily Functions for pegas
The first three functions extract information on loci, expand.genotype creates a table of all possible genotypes given a set of alleles, proba.genotype calculates expected probabilities of genotypes under Hardy–Weinberg equilibrium, and the last two functions test whether a locus is a SNP or whether a gentotype is phased.
● Data Source:
CranContrib
● Keywords: manip
● Alias: expand.genotype, getAlleles, getGenotypes, getPloidy, is.phased, is.snp, proba.genotype
●
0 images
|
VCFloci
(Package: pegas) :
Information From VCF Files
These functions help to extract information from VCF files and to select which loci to read with read.vcf.
● Data Source:
CranContrib
● Keywords: IO, manip
● Alias: VCFheader, VCFlabels, VCFloci, getINFO, is.snp.VCFinfo, print.VCFinfo, rangePOS, selectQUAL
●
0 images
|
nuc.div
(Package: pegas) :
Nucleotide Diversity
This function computes the nucleotide diversity from a sample of DNA sequences or a set of haplotypes.
● Data Source:
CranContrib
● Keywords: manip, univar
● Alias: nuc.div, nuc.div.DNAbin, nuc.div.haplotype
●
0 images
|
|
This function estimates the population parameter THETA from a genealogy (coded a as phylogenetic tree) under the coalescent.
● Data Source:
CranContrib
● Keywords: models
● Alias: theta.tree
●
0 images
|
providing 
.