| snp.data-class {GenABEL} | R Documentation |
This class contains objects holding large arrays of single nucleotide polymorphism (SNP) genotypes
nbytes:nids:male:idnames:nsnps:snpnames:chromosome:coding:strand:map:gtps:snp.mx-class object used to store genotypessignature(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.signature(from = "snp.data", to = "numeric"):
map to codes 0, 1, 2, or NAsignature(from = "snp.data", to =
"character"): map to actual nucleotide codes, e.g. "A/A", "A/G", "G/G", ""signature(from = "snp.data", to =
"genotype"): map to data frame with genotype-class
data, for later use with package geneticssignature(from = "snp.data", to =
"hsgeno"): map to data frame with allelic data frame,
for later use with package haplo.statssignature(object = "snp.data"): shows the object.
Take care that the objects are usually very large!signature(object = "snp.data"): calculate
allele frequencies, genotype frequencies, and chi-square tests for
Hardy-Weinberg equilibrium. Results are returned as a dataframeYurii Aulchenko
gwaa.data-class,
snp.data,
snp.mx-class
data(srdta)
class(srdta)
x <- srdta@gtdata
class(x)
x@nids
x@nsnps
x@idnames[1:12]
x@male[1:12]
x@male[c("p1","p2","p3","p4")]
x@snpnames[1:4]
x@chromosome[1:4]
x@map[1:4]
n4 <- c("rs18","rs655")
n4
x@map[n4]
n4 <- c("rs18","rs65")
n4
x@map[n4]
x@chromosome[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")])