snp.names: extracts names of SNPs in a region

In GenABEL: genome-wide SNP association analysis

Description

Based on boundary conditions specified and (or) chromosome selects SNP names in the region

Usage

snp.names(data, begin, end, chromosome)

Arguments

data	object of class gwaa.data-class, snp.data-class, scan.gwaa-class or check.marker-class
begin	Start position (or name of the first SNP)
end	End-position or name of last SNP
chromosome	Chromosome code

Details

Any of the arguments, except the data can be missing

Value

A vector of names of SNPs located in the region

Author(s)

Yurii Aulchenko

See Also

snp.data-class

Examples

require(GenABEL.data)
data(srdta)
snp.names(srdta, begin = 50000, end = 100000)
snp.names(srdta, begin = 50000, end = 100000, chromosome = "1")

# does not make sense with these data:
snp.names(srdta, begin = 50000, end = 100000, chromosome = "X") 

# again makes sense: 
snp.names(srdta, end = 100000)
snp.names(srdta, begin = 2200000)

# show summary for SNPs in region between 50,000 and 100,000
a <- snp.names(srdta, begin = 50000, end = 100000)
summary(srdta@gtdata[,a])

GenABEL documentation built on May 30, 2017, 3:36 a.m.