pergola: Toolbox for Polyploid Genetic Data

Provides tools for linkage mapping in polyploids. It implements the method PERGOLA, which is a fast, deterministic method to calculate the order of markers in a linkage group.

Author
Fabian Grandke [aut, cre], Dirk Metzler [ths]
Date of publication
2016-04-03 16:29:32
Maintainer
Fabian Grandke <grafabian@gmail.com>
License
GPL-3
Version
1.0
URLs

View on CRAN

Man pages

add_offset
Add offset
allTrees
Creates all trees for distance
bases2genotypes
Transform bases into genotypes
calcRec
Recombination frequencies computation
calcSarf
Calculates the SARF value of given input.
calcSarfDist
Calculates SARF
findChr
Find most equal chromosome in other map
getLeaves
Leaves from subtree
getNode
Get Node for leave
getSubtree
Subtrees from tree
makealtord
Creates vectors with highly distant neighbors
maketangle
Create a gray scale tanglegram
map2dend
Transforming a map into a dendrogram
pairwRF
Pairwise recombination frequency calculation
pergola
Toolbox for polyploid genetic data
plotChr
Plotting one or two linkage maps
plotRf
Plot recombination frequencies
pullMap
Creates map object
sarfExt
Extends SARF criterion to neighborhood
shuffleInput
Randomize marker order and alleles within samples In...
simHexa
Hexaploid F2 population
simTetra
Tetraploid F2 population
sortLeafs
Chromosome wise leaf ordering
splitChr
Split markers into chromosomes
swapChrs
Swap chromosomes
switchChr
Switch Chromosomes
switchChrs
Switch Chromosomes
switchEntries
Switches entries in hclust object

Files in this package

pergola
pergola/inst
pergola/inst/doc
pergola/inst/doc/my-vignette.html
pergola/inst/doc/my-vignette.Rmd
pergola/inst/doc/my-vignette.R
pergola/NAMESPACE
pergola/data
pergola/data/simHexa.rda
pergola/data/simTetra.rda
pergola/R
pergola/R/preprocess.R
pergola/R/plot.R
pergola/R/sort.R
pergola/R/map.R
pergola/R/data.R
pergola/R/unique.R
pergola/R/recombination.R
pergola/R/split.R
pergola/R/pergola_package.R
pergola/vignettes
pergola/vignettes/my-vignette.Rmd
pergola/MD5
pergola/build
pergola/build/vignette.rds
pergola/DESCRIPTION
pergola/man
pergola/man/getNode.Rd
pergola/man/getSubtree.Rd
pergola/man/sortLeafs.Rd
pergola/man/switchChr.Rd
pergola/man/simHexa.Rd
pergola/man/pergola.Rd
pergola/man/plotRf.Rd
pergola/man/shuffleInput.Rd
pergola/man/maketangle.Rd
pergola/man/simTetra.Rd
pergola/man/splitChr.Rd
pergola/man/calcSarf.Rd
pergola/man/bases2genotypes.Rd
pergola/man/switchEntries.Rd
pergola/man/findChr.Rd
pergola/man/allTrees.Rd
pergola/man/map2dend.Rd
pergola/man/calcSarfDist.Rd
pergola/man/add_offset.Rd
pergola/man/makealtord.Rd
pergola/man/swapChrs.Rd
pergola/man/sarfExt.Rd
pergola/man/pullMap.Rd
pergola/man/pairwRF.Rd
pergola/man/switchChrs.Rd
pergola/man/getLeaves.Rd
pergola/man/plotChr.Rd
pergola/man/calcRec.Rd