divide.autoMarkers {polySegratio}R Documentation

Divide markers by parental type

Description

Given markers (or more correctly dominant 1,0) marker data and return list object of containing markers data split according to parental alleles, namely 1,0 for each parent and 1,1 for both parents

Usage

divide.autoMarkers(markers, description = paste("Markers split for",
deparse(substitute(markers))), parent.cols = c(1, 2),
extra.cols = NULL, cols.drop = c(parent.cols, extra.cols))

Arguments

markers matrix of 1, 0, NA indicating marker alleles where rownames are markernames, column names are progeny names
description text containing a description for printing
parent.cols column(s) for parental markers (default: 1,2)
extra.cols extra column(s) to be subsetted (default: NULL)
cols.drop columns to be dropped from markers before splitting data which can be set to NULL if no columns are to be dropped (Default: c(parent.cols,extra.cols))

Value

Returns S3 class divideAutoMarkers containing

p10, p01, p11 lists for where the first, second components are heterozygous for parents 1, 2 and both resp. Each list contains
    description
    text containing a description for printing
    parent
    label for parent
    markers
    markers for specified parental type (including parents etc)
    extras
    extra columns subsetted (if specified)
    seg.ratios
    segregation ratios as class segRatio

Author(s)

Peter Baker p.baker1@uq.edu.au

See Also

segRatio, sim.autoCross

Examples


p2 <- sim.autoCross(4,
dose.proportion=list(p01=c(0.7,0.3),p10=c(0.7,0.3),
                     p11=c(0.6,0.2,0.2)))
print(p2)

ss <- divide.autoMarkers(p2$markers)

print(ss)

[Package polySegratio version 0.2-3 Index]