DSPRgenos: DSPR genotype probabilities

In egking/DSPRqtl: Analysis of DSPR phenotypes in R

Description

Function to generate genotype probabilities across the genome for a given DSPR dataset. This function is most useful for those wishing to fit their own models.

Usage

DSPRgenos(design, phenotype.dat, id.col, output = "list")

Arguments

design	a character string. For inbred RIL designs: 'inbredA', 'inbredB'. For cross designs: AAcross, BBcross, or 'ABcross'. A and B refer to the pA and pB set of DSPR RILs.
phenotype.dat	data.frame containing phenotype data. For inbred designs, there must be a column of numeric RIL ids (must be named patRIL). For cross designs, there must be both a patRIL and matRIL column specifying the maternal and paternal RIL ids. Cross designs also require a sex column for correct specification of the genotypes on the X chromosome.
id.col	a character string identifying the name of the column containing unique ids for the samples. e.g. for an inbred design, the patRIL column can be used as the id.
output	a character string identifying the preferred format for the output of genolist. Options are 'list' or 'array'. Default is 'list'.

Value

A list containing:

genolist	a list containing the matrix of additive genotype probabilities at each position in the genome. The list is in the same order as the list of positions described below. Column names are the different DSPR haplotypes and row names are the unique ids provided in id.col. Alternatively, if output='array', the output is a 3 dimensional array [samples, haplotypes, positions]. Haplotypes and samples are named while positions are in the order of the list of positions described below.
positions	a data.frame containing regularly spaced positions (every 10KB) in the genome where the genotype probabilities are calculated. Columns are: chr = chromosome, Ppos = physical position (zero offset), Gpos = genetic position, Gaxis = cumulative genetic position.
phenotype	the phenotype.dat data.frame ordered by the specified id column and in the same order as the genotype information at each position in the genome in the geno list described above

Author(s)

Elizabeth King ([e-mail])

egking/DSPRqtl documentation built on May 16, 2019, 12:14 a.m.