cs: Chromosome Splitter

In hsphase: Phasing, Pedigree Reconstruction, Sire Imputation and Recombination Events Identification of Half-sib Families Using SNP Data

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)

hsphase documentation built on May 29, 2024, 2:20 a.m.