PolyHaplotyper (version 1.0.1)

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

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

Value

a data.frame in the described ShesisPlus input format

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

Examples

# NOT RUN {
data(PolyHaplotyper_small)
SSPin <- make.ShesisPlus.input(mrkDosage=phdos, markers=phblocks[[1]],
                              ploidy=6)
SSPin[1:6,1:8]
# }