Splits the genotype list generated by hss into chromosomes based on a map file/data.frame and orders SNPs by chromosomal position.
Usage
cs(halfsib, mapPath, separator = " ")
Value
Returns a list of matrices, the number of elements in this list is the number of half-sib families multiplied by the number of chromosomes.
Arguments
halfsib
list. List of genotype matrices (one family per list item).
mapPath
character path to the map file (column 1 -> SNP names, column 2 -> chromosome name and column 3 -> SNP position in base pairs) or, alternatively, the name of a dataframe with the mapping information (in the same format)
separator
character. Field separator for the map file.
Details
The map file should include only the chromosomes that will be analyzed. For example, the Y and X chromosomes should be excluded (and others optionally). Names of each element in the list can be used for further categorization.
The header must be "Name Chr Position".