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

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

Description

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

Usage

make.ShesisPlus.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 the output file: this will contain the data in the ShesisPlus format (the saved data.frame is also the return value). If "" (default) no file is written

Details

ShesisPlus needs the data formatted as: 1 column with names of individuals, 1 column with the phenotypes (with missing values represented as "NA"), and for each of the selected markers <ploidy> columns, with the (unphased) marker alleles. Here we use only biallelic markers; their alleles are indicated by 1 and 2 for the ref and alt allele, and 0 for missing data.
The contents of file fname can be pasted into the input data box of the ShesisPlus web interface at http://shesisplus.bio-x.cn/SHEsis.html

Value

a data.frame in the described ShesisPlus input format

Examples

data(PolyHaplotyper_small)
SSPin <- make.ShesisPlus.input(mrkDosage=phdos, markers=phblocks[[1]],
                              ploidy=6)
SSPin[1:6,1:8]

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