divide.autoMarkers function

Divide markers by parental type

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

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))

Returns

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)