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

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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

  • descriptiontext containing a description for printing

  • parentlabel for parent

  • markersmarkers for specified parental type (including parents etc)

  • extrasextra columns subsetted (if specified)

  • seg.ratiossegregation ratios as class segRatio

Author(s)

Peter Baker p.baker1@uq.edu.au

See Also

segRatio, sim.autoCross

Examples

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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)