cs {hsphase}

Chromosome Splitter

Description

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

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".

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.

Examples

# Please run demo(hsphase)