Class "snp.data"

snp.data-class {GenABEL}R Documentation

Class "snp.data"

Description

This class contains objects holding large arrays of single nucleotide polymorphism (SNP) genotypes

Slots

nbytes:
number of bytes used to store data on a SNP
nids:
number of people
male:
male code
idnames:
ID names
nsnps:
number of SNPs
snpnames:
list of SNP names
chromosome:
list chromosomes corresponding to SNPs
coding:
list of nucleotide coding for the SNPs
strand:
strands of the SNPs
map:
list SNPs' positions
gtps:
snp.mx-class object used to store genotypes

Methods

[
signature(x = "snp.data", i = "ANY", j = "ANY", drop = "ANY"): subset operations. x[i,j] will select people listed in i and SNPs listed in j.
coerce
signature(from = "snp.data", to = "numeric"): map to codes 0, 1, 2, or NA
coerce
signature(from = "snp.data", to = "character"): map to actual nucleotide codes, e.g. "A/A", "A/G", "G/G", ""
coerce
signature(from = "snp.data", to = "genotype"): map to data frame with genotype-class data, for later use with package genetics
coerce
signature(from = "snp.data", to = "hsgeno"): map to data frame with allelic data frame, for later use with package haplo.stats
show
signature(object = "snp.data"): shows the object. Take care that the objects are usually very large!
summary
signature(object = "snp.data"): calculate allele frequencies, genotype frequencies, and chi-square tests for Hardy-Weinberg equilibrium. Results are returned as a dataframe
annotation
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts annotation
idnames
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts id names
snpnames
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts snp names
nids
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts number of ids
nsnps
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts number of snps
map
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts map
chromosome
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts chromosome
strand
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts strand
coding
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts coding
refallele
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts reference allele
effallele
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts effective allele
male
signature(object = "gwaa.data"), signature(object = "snp.data"): extracts male indicator

Author(s)

Yurii Aulchenko

See Also

gwaa.data-class, snp.data, snp.mx-class

Examples

data(srdta)
class(srdta)
x <- srdta@gtdata
class(x)
nids(x)
nsnps(x)
idnames(x)[1:12]
male(x)[1:12]
male(x)[c("p1","p2","p3","p4")]
snpnames(x)[1:4]
chromosome(x)[1:4]
map(x)[1:4]
n4 <- c("rs18","rs655")
n4
map(x)[n4]
n4 <- c("rs18","rs65")
n4
map(x)[n4]
chromosome(x)[n4]
x[1:12,1:4]
summary(x[,1:10])
as.numeric(x[1:12,1:4])
as.numeric(x[c("p1","p3","p4"),c("rs18","rs65")])
as.character(x[c("p1","p3","p4"),c("rs18","rs65")])
as.genotype(x[c("p1","p3","p4"),c("rs18","rs65")])
as.hsgeno(x[c("p1","p3","p4"),c("rs18","rs65")])

[Package GenABEL version 1.6-7 Index]