impute_LA: Impute from low to high density markers by Linkage Analysis...
In jendelman/polyBreedR: Genomics-assisted breeding for polyploids (and diploids)
impute_LA R Documentation
Impute from low to high density markers by Linkage Analysis (LA)
Description
Impute from low to high density markers by Linkage Analysis
Usage
impute_LA(ped.file, high.file, low.file, low.format = "GT", out.file)
Arguments
ped.file
pedigree file for progeny
high.file
name of file with phased parental genotypes
low.file
name of VCF file with progeny
low.format
either "GT" (default) or "AD"
out.file
name of CSV output file
Details
You must have separately installed PolyOrigin and Julia for this function to work.
The high density file contains phased parental genotypes using 0|1 format. The first 3 columns are the genetic map in cM: marker, chrom, position. To output imputed data with physical rather than genetic map positions, including a fourth column named "bp". Subsequent columns are the phased parental genotypes.
VCF is assumed for the low-density file. The pedigree file has four columns: id, pop, mother, father, ploidy.
The output file contains the posterior maximum genotypes.
A temporary directory "tmp" is created to store intermediate files and then deleted.
jendelman/polyBreedR documentation built on Jan. 5, 2025, 12:13 a.m.
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| impute_LA | R Documentation |
Impute from low to high density markers by Linkage Analysis (LA)
Description
Impute from low to high density markers by Linkage Analysis
Usage
impute_LA(ped.file, high.file, low.file, low.format = "GT", out.file)
Arguments
ped.file |
pedigree file for progeny |
high.file |
name of file with phased parental genotypes |
low.file |
name of VCF file with progeny |
low.format |
either "GT" (default) or "AD" |
out.file |
name of CSV output file |
Details
You must have separately installed PolyOrigin and Julia for this function to work.
The high density file contains phased parental genotypes using 0|1 format. The first 3 columns are the genetic map in cM: marker, chrom, position. To output imputed data with physical rather than genetic map positions, including a fourth column named "bp". Subsequent columns are the phased parental genotypes.
VCF is assumed for the low-density file. The pedigree file has four columns: id, pop, mother, father, ploidy.
The output file contains the posterior maximum genotypes.
A temporary directory "tmp" is created to store intermediate files and then deleted.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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