make.SATlotyper.input: convert PolyHaplotyper marker data to SATlotyper format

In PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Description

convert PolyHaplotyper marker data (input) to SATlotyper format for a single haploblock.

Usage

make.SATlotyper.input(mrkDosage, indiv=NULL, markers,
ploidy, phenotype=0, fname)

Arguments

mrkDosage	matrix or data.frame of allele dosages; same as input for inferHaplotypes. Markers are in rows, individuals in columns, each cell has a marker dosage. All marker dosages must be in 0:ploidy or NA
indiv	the names of the individuals to include in the ShesisPlus input data. Default NULL includes all individuals
markers	character vector with the names of the markers in the haploblock; all must occur in mrkDosage
ploidy	single integer: the ploidy level
phenotype	vector with the phenotypes of all individuals, in order of the columns of dosmat; default 0
fname	filename of a *.csv output file: this will contain the data in the SATlotyper format (the saved data.frame is also the return value). If "" no file is written

Value

a data.frame in the SATlotyper input format: a header row with "Genotype" and the marker names, and one row per individual with the individual name plus for each marker the genotype as a sorted string of <ploidy> A's and B's, or <ploidy> N's

Examples

data(PolyHaplotyper_small)
SATin <- make.SATlotyper.input(mrkDosage=phdos, markers=phblocks[[1]],
                              ploidy=6, fname="")
head(SATin)

PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.