snpgdsOption: Option settings: chromosome coding, etc

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Description

Return an option list used by the SNPRelate package or a GDS file

Usage

snpgdsOption(gdsobj=NULL, autosome.start=1L, autosome.end=22L, ...)

Arguments

gdsobj	an object of class SNPGDSFileClass, a SNP GDS file
autosome.start	the starting index of autosome
autosome.end	the ending index of autosome
...	optional arguments for new chromosome coding

Value

A list

Author(s)

Xiuwen Zheng

Examples

# define the new chromosomes 'Z' and 'W'
snpgdsOption(Z=27L, W=28L)


# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())

snpgdsOption(genofile)

# close the genotype file
snpgdsClose(genofile)

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.