This function splits the genotypes list generated by hss into the different chromosomes based on a map file and orders SNP based on chromosomal position.
Usage
cs(halfsib, mapPath, separator = " ")
Arguments
halfsib
List list with matrices of half-sib genotypes, 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 separator character used in the the map file
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.
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".