snp {SNPassoc}

SNP object

Description

snp creates an snp object

is returns TRUE if x is of class 'snp'

as attempts to coerce its argument into an object of class 'snp'

reorder change the reference genotype

summary gives a summary for an object of class 'snp' including genotype and allele frequencies and an exact thest of Hardy-Weinberg equilibrium

plot gives a summary for an object of class 'snp' including genotype and allele frequencies and an exact thest of Hardy-Weinberg equilibrium in a plot. Barplot or pie are allowed

[.snp is a copy of [.factor modified to preserve all attributes

Usage

  snp(x, sep = "/", name.genotypes, reorder="common", 
    remove.spaces = TRUE, allow.partial.missing = FALSE) 

  is.snp(x)
 
  as.snp(x, ...)

  ## S3 method for class 'snp'
additive(o)

Arguments

x

either an object of class 'snp' or an object to be converted to class 'snp'

sep

character separator used to divide alleles when x is a vector of strings where each string holds both alleles. The default is "/". See below for details.

name.genotypes

the codes for the genotypes. This argument may be useful when genotypes are coded using three different codes (e.g., 0,1,2 or hom1, het, hom2)

reorder

how should genotypes within an individual be reordered. Possible values are 'common' or 'minor'. The default is reorder="common". In that case, alleles are sorted within each individual by common homozygous.

remove.spaces

logical indicating whether spaces and tabs will be removed from the genotypes before processing

allow.partial.missing

logical indicating whether one allele is permitted to be missing. When set to 'FALSE' both alleles are set to 'NA' when either is missing.

o

an object of class 'snp' to be coded as a linear covariate: 0,1,2

...

optional arguments

Details

SNP objects hold information on which gene or marker alleles were observed for different individuals. For each individual, two alleles are recorded.

The snp class considers the stored alleles to be unordered , i.e., "C/T" is equivalent to "T/C". It assumes that the order of the alleles is not important.

When snp is called, x is a character vector, and it is assumed that each element encodes both alleles. In this case, if sep is a character string, x is assumed to be coded as "Allele1<sep>Allele2". If sep is a numeric value, it is assumed that character locations 1:sep contain allele 1 and that remaining locations contain allele 2.

additive.snp recodes the SNPs for being analyzed as a linear covariate (codes 0,1,2)

Value

The snp class extends "factor" where the levels is a character vector of possible genotype values stored coded by paste( allele1, "", allele2, sep="/")

References

JR Gonzalez, L Armengol, X Sole, E Guino, JM Mercader, X Estivill, V Moreno. SNPassoc: an R package to perform whole genome association studies. Bioinformatics, 2007;23(5):654-5.

See Also

association

Examples

# some examples of snp data in different formats

dat1  <- c("21", "21", "11", "22", "21",
                    "22", "22", "11", "11", NA)
ans1  <- snp(dat1,sep="")
ans1

dat2 <- c("A/A","A/G","G/G","A/G","G/G",
                    "A/A","A/A","G/G",NA)
ans2  <- snp(dat2,sep="/")
ans2

dat3 <- c("C-C","C-T","C-C","T-T","C-C",
                    "C-C","C-C","C-C","T-T",NA)
ans3 <- snp(dat3,sep="-")
ans3


dat4 <- c("het","het","het","hom1","hom2",
                    "het","het","hom1","hom1",NA)
ans4 <- snp(dat4,name.genotypes=c("hom1","het","hom2"))
ans4


# summary 
summary(ans3)

# plots

plot(ans3)
plot(ans3,type=pie)
plot(ans3,type=pie,label="SNP 10045")