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PolyHaplotyper (version 1.0.1)

Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

Infer the genetic composition of individuals in terms of haplotype dosages for a haploblock, based on bi-allelic marker dosages, for any ploidy level. Reference: Voorrips and Tumino: PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data. Submitted to BMC Bioinformatics (2021).

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Version

Install

install.packages('PolyHaplotyper')

Monthly Downloads

192

Version

1.0.1

License

GPL-2

Maintainer

Roeland Voorrips

Last Published

June 17th, 2021

Functions in PolyHaplotyper (1.0.1)

compareHapMrkDosages

compare haplotyping results with observed markers dosages
calcStatistics

calculate some statistics of the solutions of all haploblocks
allhap

Find all possible haplotypes
build_ahccompletelist

generate a list with all haplotype combinations
calcMrkHaptable

produce a table of nr of markers vs nr of haplotypes
checkmrkDosage

check a marker dosages matrix or data.frame
compareHapresults

compare two haplotyping results
allHaplotypes

get all haplotypes for the given markers
demo_ped

pedigree
demo_snpdos

dosages of SNP alleles
make.Happyinf.input

convert PolyHaplotyper input data to Happy-inf format
hapcomb2hapdos

convert haplotype combinations to haplotype dosages
getGameteFreqs

get all gametes and their frequencies for a parental haplotype combination
make.SATlotyper.input

convert PolyHaplotyper marker data to SATlotyper format
getFSfreqs

get all FS haplotype combinations expected from two parental haplotype combinations, with their frequencies
phFS

members of FS families
expandHapdos

Add dropped rows back to haplotype dosage matrix
phblocks

List of markers per haploblock
hapdos2mrkdos

calculate the marker dosages resulting from haplotype dosage combinations
padded

pad an integer (prefix with zeroes to a fixed length)
overviewByFS

generate an overview of the results by haploblock and by FS family
hapdos2hapcomb

convert haplotype dosages to haplotype combinations
totHapcombCount

calculate the total nr of possible haplotype combinations
showOneFS

show marker and haplotype dosages for one FS family
make.ShesisPlus.input

convert PolyHaplotyper marker data to ShesisPlus format
pedigreeHapCheck

check the consistency of haploblock genotypes over a pedigree
pedigreeSim2PH

convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages
usedhap

Find all used (inferred) haplotypes
phped

pedigree
inferHaplotypes

infer haplotypes for one or more haploblocks
phpar

parents of FS families
haploblock_df2list

convert a haploblock-defining data frame to a list
mrkdos2mrkdid

get marker dosage IDs from marker dosages
mrkdid2mrkdos

get the marker dosages from mrkdids (marker dosage IDs)
phdos

dosages of SNP alleles
phresults

haplotyping results
read.ShesisPlus.output

Read the haplotyping results from the ShesisPlus output
mergeReplicates

merge replicate samples in dosage matrix
run.SATlotyper

A simple interface to run SATlotyper
read.SATlotyper.output

read the haplotyping results from the SATlotyper output
read.Happyinf.output

read the haplotyping results from the Happy-inf output