Objects can be created by calls of the form new("bed.matrix", ...).
Slots
ped:
data.frame containing information for each individual: famid = Family ID,
id = Individual ID, father = Father ID, mother = Mother ID, sex = Sex and pheno = Phenotype.
Can also contain individuals statistic, for example: N0, N1 and N2 = Number of genotypes equal to 0, 1 and 2 respectively,
NAs = Number of missing genotypes, callrate = Individual callrate.
snps:
data.frame containing information for each SNP: chr = Chromosome, id = SNP ID,
dist = Genetic Distance, pos = Physical position, A1 = Reference Allele, A2 = Alternative Allele.
Can also contain SNPs statistic, for example: N0, N1 and N2 = Number of genotypes equal to 0, 1 and 2 repectively,
NAs = Number of missing genotypes, callrate = SNP callrate, maf = Minor allele frequency), hz = heterozygosity
bed:
externalptr (pointing to the genotype matrix).
p:
vector or NULL for allelic frequencies.
mu:
vector or NULL for genotype means (usually mu = 2*p).
sigma:
vector or NULL for genotypic standard deviation
standardize_p:
logical. If TRUE, the genotype matrix is standardized using means 2*p
and genotypic standard deviation sqrt(2*p*(1-p))
standardize_mu_sigma:
logical. If TRUE, the genotype matrix is standardize using means
mu and genotypic standard deviation sigma.
Methods
[
signature(x = "bed.matrix", i = "numeric" or "logical" or "missing", j = "numeric" or "logical" or "missing", drop = "missing"):
Extract a sub-matrix (a new bed.matrix).
%*%
signature(x = "bed.matrix", y = "matrix" or "vector"):
Right matrix multiplication of the genotype matrix (possibly centered and reduced) with a matrix or a vector.
%*%
signature(x = "matrix" or "vector", y = "bed.matrix"):
Left matrix multiplication of the genotype matrix with a matrix or a vector.
as.matrix
signature(x = "bed.matrix"):
Convert a bed.matrix into a matrix.
The resulting matrix can be huge, use this method only for a small bed.matrix!
standardize
signature(x = "bed.matrix"):
Get the standardize parameter of bed.matrix. Can be "none", "p" or "mu_sigma".
standardize<-
signature(x = "bed.matrix"):
Set the standardize parameter of a bed.matrix.
dim
signature(x = "bed.matrix"):
Get the number of individuals (rows) and the number of SNPs (columns).
head
signature(x = "bed.matrix"):
Print the head of the genotype matrix of a bed.matrix object.
mu
signature(x = "bed.matrix"):
Get the mu slot of a bed.matrix.
mu<-
signature(x = "bed.matrix"):
Set the mu slot of a bed.matrix.
p
signature(x = "bed.matrix"):
Get the p slot of a bed.matrix.
p<-
signature(x = "bed.matrix"):
Set the p slot of a bed.matrix.
show
signature(object = "bed.matrix"):
Displays basic information about a bed.matrix.
sigma
signature(x = "bed.matrix"):
Get the sigma slot of a bed.matrix.
sigma<-
signature(x = "bed.matrix"):
Set the sigma slot of a bed.matrix.
cbind
signature(... = "bed.matrix"):
Combine a sequence of bed.matrix by columns.
rbind
signature(... = "bed.matrix"):
Combine a sequence of bed.matrix by rows.
Author(s)
Herv<c3><83><c2><a9> Perdry and Claire Dandine-Roulland
showClass("bed.matrix")
# Conversion example
data(LCT)
x1 <- as(LCT.gen, "bed.matrix")
x1
head(x1@ped)
head(x1@snps)
# the function as.bed.matrix is an alternative
x2 <- as.bed.matrix(LCT.gen, LCT.fam, LCT.bim)
x2
head(x2@ped)
head(x2@snps)