PolyOriginR

PolyOriginR is a wrapper of PolyOrigin.jl (https://github.com/chaozhi/PolyOrigin.jl), for haplotye reconstruction in polyploid multiparental pouplations.

Installation

First download and install Julia (>v1.5,64-bit)available at https://julialang.org/. Then install the development version of PolyOriginR from GitHub with:

# install.packages("devtools")
devtools::install_github("chaozhi/PolyOriginR")

Example

library(PolyOriginR)
polyOriginR("geno.csv","ped.csv",juliapath="C:/path/to/bin/julia.exe",workdir="workdir")

Here juliapath is the absolute path to julia.exe, and workdir is the directory for input and output files. See R script and input files in the "inst/example" folder.

Usage

polyOriginR(
  genofile,
  pedfile,
  juliapath = "",
  epsilon = 0.01,
  seqerr = 0.001,
  chrpairing_phase = 22,
  chrpairing = 44,
  chrsubset = NULL,
  snpthin = 1,
  nworker = 1,
  delsiglevel = 0.05,
  maxstuck = 5,
  maxiter = 30,
  minrun = 3,
  maxrun = 10,
  byparent = TRUE,
  refhapfile = "nothing",
  correctthreshold = 0.15,
  refinemap = FALSE,
  refineorder = FALSE,
  maxwinsize = 50,
  inittemperature = 4,
  coolingrate = 0.5,
  stripdis = 20,
  maxepsilon = 0.5,
  skeletonsize = 50,
  isphysmap = FALSE,
  recomrate = 1,
  isplot = FALSE,
  workdir = getwd(),
  outstem = "outstem",
  verbose = TRUE
)

Arguments

Argument	Description
`genofile`	Input genotypic data for parents and offspring
`pedfile`	Input breeding pedigree
`juliapath`	Path to julia.exe, Default: ''
`epsilon`	genotyping error probability, Default: 0.01
`seqerr`	sequencing read error probability for GBS data, Default: 0.001
`chrpairing_phase`	chromosome pairing in parental phasing, with 22 being only bivalent formations and 44 being bi- and quadri-valent formations, Default: 22
`chrpairing`	chromosome pairing in offspring decoding, with 22 being only bivalent formations and 44 being bivalent and quadrivalent formations, Default: 44
`chrsubset`	subset of chromosomes, c(1,10) denotes first and tenth chromosomes, and NULL for all chromosomes, Default: NULL
`snpthin`	subset of markers, take every snpthin-th markers, Default: 1
`nworker`	number of parallel workers for computing among chromosomes, nonparallel if nworker=1, Default: 1
`delsiglevel`	significance level for deleting markers, Default: 0.05
`maxstuck`	the max number of consecutive iterations that are rejected in a phasing run, Default: 5
`maxiter`	the max number of iterations in a phasing run, Default: 30
`minrun`	if the min number of phasing runs that are at the same local maximimum or have the same parental phases reaches minrun, phasing algorithm will stop before reaching the maxrun, Default: 3
`maxrun`	the max number of phasing runs, Default: 10
`byparent`	if TRUE, update parental phases parent by parent, Default: TRUE
`refhapfile`	reference haplotype file for setting absolute parental phases, Default: 'nothing'
`correctthreshold`	a candidate marker is selected for parental error correction if the fraction of offspring genotypic error >= correctthreshold, Default: 0.15
`refinemap`	if TRUE, refine marker map, Default: FALSE
`refineorder`	if TRUE, refine marker mordering, valid only if refinemap=TRUE, Default: FALSE
`maxwinsize`	max size of sliding windown in map refinning, Default: 50
`inittemperature`	initial temperature of simulated annealing in map refinning, Default: 4
`coolingrate`	cooling rate of annealing temperature in map refinning, Default: 0.5
`stripdis`	a chromosome end in map refinement is removed if it has a distance gap > stripdis(centiMorgan) and it contains less than 5% markers, Default: 20
`maxepsilon`	markers in map refinement are removed it they have error rates > maxepsilon, Default: 0.5
`skeletonsize`	the number of markers in the skeleton map that is used to reduce map length inflation by subsampling markers, Default: 50
`isphysmap`	TRUE, if input marker map in genofile is physical map, Default: FALSE
`recomrate`	Recombination rate in cM/Mpb, Default: 1
`isplot`	TURE, if plot haploprob, Default: FALSE
`workdir`	Work directory, Default: getwd()
`outstem`	Stem of output files, Default: 'outstem'
`verbose`	TURE, if print details, Default: TRUE

Details

PolyOriginR is implemented via PolyOriginCmd, which uses PolyOrigin.jl by a command line.

Value

Return 0 if success, and export output files.

Argument	Description
`outstem.log`	log file
`outstem_maprefined.csv`	same as input genofile except that marker map being refined
`outstem_parentphased.csv`	same as input genofile exceptthat parents being phased
`outstem_parentphased_corrected.csv`	exported if there exist detected parental errors
`outstem_polyancestry.csv`	genoprob and estimation of valent configurations
`outstem_genoprob.csv`	a simplified version of outstem_polyancestry.csv
`outstem_postdoseprob.csv`	posterior dosage probabilities for all offspring
`outstem_plots`	a folder contains plots of condprob for all offspring if isplot = true

Citing PolyOrigin

If you use PolyOriginR in your analyses and publish your results, please cite the article:

Zheng C, Amadeu RR, Munoz PR, and Endelman JB. 2020. Haplotype Reconstruction in Connected Tetraploid F1 Populations. https://www.biorxiv.org/content/10.1101/2020.12.18.423519v1.