allhap |
Find all possible haplotypes |
allHaplotypes |
get all haplotypes for the given markers |
build_ahccompletelist |
generate a list with all haplotype combinations |
calcMrkHaptable |
produce a table of nr of markers vs nr of haplotypes |
calcStatistics |
calculate some statistics of the solutions of all haploblocks |
checkmrkDosage |
check a marker dosages matrix or data.frame |
compareHapMrkDosages |
compare haplotyping results with observed markers dosages |
compareHapresults |
compare two haplotyping results |
demo_ped |
pedigree |
demo_snpdos |
dosages of SNP alleles |
expandHapdos |
Add dropped rows back to haplotype dosage matrix |
getFSfreqs |
get all FS haplotype combinations expected from two parental haplotype combinations, with their frequencies |
getGameteFreqs |
get all gametes and their frequencies for a parental haplotype combination |
hapcomb2hapdos |
convert haplotype combinations to haplotype dosages |
hapdos2hapcomb |
convert haplotype dosages to haplotype combinations |
hapdos2mrkdos |
calculate the marker dosages resulting from haplotype dosage combinations |
haploblock_df2list |
convert a haploblock-defining data frame to a list |
inferHaplotypes |
infer haplotypes for one or more haploblocks |
make.Happyinf.input |
convert PolyHaplotyper input data to Happy-inf format |
make.SATlotyper.input |
convert PolyHaplotyper marker data to SATlotyper format |
make.ShesisPlus.input |
convert PolyHaplotyper marker data to ShesisPlus format |
mergeReplicates |
merge replicate samples in dosage matrix |
mrkdid2mrkdos |
get the marker dosages from mrkdids (marker dosage IDs) |
mrkdos2mrkdid |
get marker dosage IDs from marker dosages |
overviewByFS |
generate an overview of the results by haploblock and by FS family |
padded |
pad an integer (prefix with zeroes to a fixed length) |
pedigreeHapCheck |
check the consistency of haploblock genotypes over a pedigree |
pedigreeSim2PH |
convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages |
phblocks |
List of markers per haploblock |
phdos |
dosages of SNP alleles |
phFS |
members of FS families |
phpar |
parents of FS families |
phped |
pedigree |
phresults |
haplotyping results |
read.Happyinf.output |
read the haplotyping results from the Happy-inf output |
read.SATlotyper.output |
read the haplotyping results from the SATlotyper output |
read.ShesisPlus.output |
Read the haplotyping results from the ShesisPlus output |
run.SATlotyper |
A simple interface to run SATlotyper |
showOneFS |
show marker and haplotype dosages for one FS family |
totHapcombCount |
calculate the total nr of possible haplotype combinations |
usedhap |
Find all used (inferred) haplotypes |