pergola: Toolbox for Polyploid Genetic Data
Version 1.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorFabian Grandke [aut, cre], Dirk Metzler [ths]
Date of publication2016-04-03 16:29:32
MaintainerFabian Grandke <grafabian@gmail.com>
LicenseGPL-3
Version1.0
URL http://github.com/grafab/pergola
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("pergola")

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

Functions

add_offset Man page Source code
allTrees Man page Source code
bases2genotypes Man page Source code
calcRec Man page Source code
calcSarf Man page Source code
calcSarfDist Man page Source code
findChr Man page Source code
getLeaves Man page Source code
getNode Man page Source code
getSubtree Man page Source code
makealtord Man page Source code
maketangle Man page Source code
map2dend Man page Source code
pairwRF Man page Source code
pergola Man page
pergola-package Man page
plotChr Man page Source code
plotRf Man page Source code
pullMap Man page Source code
sarfExt Man page Source code
shuffleInput Man page Source code
simHexa Man page
simTetra Man page
sortLeafs Man page Source code
splitChr Man page Source code
swapChrs Man page Source code
switchChr Man page Source code
switchChrs Man page Source code
switchEntries Man page Source code

Files

inst
inst/doc
inst/doc/my-vignette.html
inst/doc/my-vignette.Rmd
inst/doc/my-vignette.R
NAMESPACE
data
data/simHexa.rda
data/simTetra.rda
R
R/preprocess.R
R/plot.R
R/sort.R
R/map.R
R/data.R
R/unique.R
R/recombination.R
R/split.R
R/pergola_package.R
vignettes
vignettes/my-vignette.Rmd
MD5
build
build/vignette.rds
DESCRIPTION
man
man/getNode.Rd
man/getSubtree.Rd
man/sortLeafs.Rd
man/switchChr.Rd
man/simHexa.Rd
man/pergola.Rd
man/plotRf.Rd
man/shuffleInput.Rd
man/maketangle.Rd
man/simTetra.Rd
man/splitChr.Rd
man/calcSarf.Rd
man/bases2genotypes.Rd
man/switchEntries.Rd
man/findChr.Rd
man/allTrees.Rd
man/map2dend.Rd
man/calcSarfDist.Rd
man/add_offset.Rd
man/makealtord.Rd
man/swapChrs.Rd
man/sarfExt.Rd
man/pullMap.Rd
man/pairwRF.Rd
man/switchChrs.Rd
man/getLeaves.Rd
man/plotChr.Rd
man/calcRec.Rd
pergola documentation built on May 19, 2017, 2:06 p.m.