R: 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

strand<-

  `signature(object = "gwaa.data")`, `signature(object = "snp.data")`: assign strand

coding

  `signature(object = "gwaa.data")`, `signature(object = "snp.data")`: extracts coding

coding<-

  `signature(object = "gwaa.data")`, `signature(object = "snp.data")`: assign 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

    require(GenABEL.data)
    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 1.8-0 Index]