fq_haplotyping_session: Function to assign haploblock alleles in pedigrees using...

In PBR/PediHaplotyper: PediHaplotyper assigns haploblock alleles based on phased marker data in pedigrees

Description

Function fq_haplotyping_session is a user-friendly wrapper for the separate steps in the imputation and allele assignment process; only the first 2 parameters need to be specified.

Usage

fq_haplotyping_session(sessionID, mapfile, 
fqparfile = "flexqtl.par", 
pedigreefile = "flexqtl.sort", 
phasedgenofile = "mhaplotypes.csv", 
oldhballelesfile = "", 
messagefile = "messages.txt", 
mrkpolymorphismfile = "mrkpolymorphism.dat", 
hballelesfile = "hballeles.dat", 
HSorighballelesfile = "orig_hballeles_byHS.dat", 
HSfinalhballelesfile = "final_hballeles_byHS.dat", 
hbstatisticsfile = "hbstatistics.dat", 
mrkstatisticsfile = "mrkstatistics.dat", 
origpedimaphbfile = "orighb.ped", 
finalpedimaphbfile = "finalhb.ped", 
origpedimapmrkfile = "origmrk.ped", 
finalpedimapmrkfile = "finalmrk.ped", 
origflexqtlhbfiles = "orighb_flexqtl", 
finalflexqtlhbfiles = "finalhb_flexqtl", 
origflexqtlmrkfiles = "origmrk_flexqtl", 
finalflexqtlmrkfiles = "finalmrk_flexqtl", 
min.allele.freq = 3, 
mv.count = FALSE, 
FQout = TRUE)

Arguments

sessionID	(Short) text string, will be prefixed to all output filenames
mapfile	Name of the input file containing the linkage map, must be specified
fqparfile	Name of the FlexQTL parameter file, by default "flexqtl.par"
pedigreefile	Name of the input file containing the pedigree and optionally phenotypic data, by default "flexqtl.sort". If this file is not available the datafile specified in the FlexQTL parameter file is used.
phasedgenofile	Name of the input file with phased marker genotypes, by default "mhaplotypes.csv"
oldhballelesfile	Name of an optional input file with haploblock alleles, the hballeles file from an earlier PediHaplotyper run
messagefile	Name of the output file that will contain messages
mrkpolymorphismfile	Name of the output file with polymorphism information for each marker
hballelesfile	Name of the output file listing the alleles of each haploblock
HSorighballelesfile	Name of the output file listing all haploblock alleles per Half-Sib at the start of the process
HSfinalhballelesfile	Name of the output file listing all haploblock alleles per Half-Sib at the end of the process
hbstatisticsfile	Name of the output file that lists the number of changes made to haploblock alleles during the process
mrkstatisticsfile	Name of the output file that lists the number of changes made to marker alleles during the process
origpedimaphbfile	Name of the output file with Pedimap data for visualizing the haploblock allele configurations at the start of the process
finalpedimaphbfile	Name of the output file with Pedimap data for visualizing the haploblock allele configurations at the end of the process
origpedimapmrkfile	Name of the output file with Pedimap data for visualizing the marker allele configurations at the start of the process
finalpedimapmrkfile	Name of the output file with Pedimap data for visualizing the marker allele configurations at the end of the process
origflexqtlhbfiles	Name of the output file with the pedigree and phased haploblock alleles at the start of the process, in FlexQTL-readable format
finalflexqtlhbfiles	Name of the output file with the pedigree and phased haploblock alleles at the end of the process, in FlexQTL-readable format
origflexqtlmrkfiles	Name of the output file with the pedigree and phased marker alleles at the start of the process, in FlexQTL-readable format
finalflexqtlmrkfiles	Name of the output file with the pedigree and phased marker alleles at the end of the process, in FlexQTL-readable format
min.allele.freq	A marker is considered sufficiently polymorphic if at least two of its alleles each occur at least this number of times (default: 3 times) in the pedigree. If not, the marker is not used in the haploblock allele assignment.
mv.count	If FALSE (default), the haploblock allele IDs consist only of a sequential number. If TRUE the IDs have the form n(x), where n is the sequential number and x is the number of missing marker alleles in this haploblock allele.
FQout	If TRUE the output will be in FlexQTL format, else in generic format.

Details

This function takes phased marker data for individuals in a pedigree, and for each haploblock (group of tightly linked markers) assigns haploblock alleles to all individuals. In the process conflicts are resolved by deleting or correcting marker alleles, and missing marker data are imputed, assuming that no within-haploblock recombination occurs over the entire pedigree. See the publication and the manual (under References) for further details.

Value

The function does not return a value but creates a series of output files in the current working directory

Author(s)

Roeland E. Voorrips, Wageningen University & Research Centre, email [e-mail]

References

Voorrips RE, Bink MCAM, Kruisselbrink JW, Koehorst-van Putten HJJ, Van de Weg WE: PediHaplotyper: Software for consistent assignment of marker haplotypes in pedigrees. Submitted to Molecular Breeding.

Website with manual and example data: https://www.wageningenur.nl/en/show/PediHaplotyper.htm

Examples

## Download the manual and example files from
## https://www.wageningenur.nl/en/show/PediHaplotyper.htm 

PBR/PediHaplotyper documentation built on Feb. 3, 2021, 12:03 a.m.