BEDMatrix: BEDMatrix-class – R documentation

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BEDMatrix-class

A Class to Extract Genotypes from a PLINK .bed File

Description

BEDMatrix is a class that maps a PLINK .bed file into memory and behaves similarly to a regular matrix by implementing key methods such as [, dim, and dimnames. Subsets are extracted directly and on-demand from the .bed file without loading the entire file into memory.

Details

The subsets extracted from a BEDMatrix object are coded as the allelic dosages of the first allele in the .bim file (A1), similarly to .raw files generated with the --recode A argument in PLINK).

Internally, this class is an S4 class with the following slots that should not be relied upon in actual code: xptr, dims, dnames, and path. The .bed file is mapped into memory using mmap on Unix and MapViewOfFile on Windows.

Slots

xptr:: An external pointer to the underlying C code.
dims:: An integer vector specifying the number of samples and variants as determined by the the accompanying .fam and .bim files or by the n and p parameters of the BEDMatrix constructor function.
dnames:: A list describing the row names and column names of the object as determined by the accompanying .fam and .bim files, or NULL if the n and p parameters of the BEDMatrix constructor function were provided.
path:: A character string containing the path to the .bed file.

Methods

[:: Extract parts of an object
dim:: Retrieve the dimension of an object
dimnames:: Retrieve the dimnames of an object
dimnames<-:: Set the dimnames of an object
as.matrix:: Turn the object into a matrix
is.matrix:: Test if the object is a matrix
length:: Get the length of an object
str:: Display the internal structure of an object
show:: Display the object

Examples

# Get the path to the example .bed file
path <- system.file("extdata", "example.bed",
                    package = "BEDMatrix")

# Create a BEDMatrix object the example .bed file
m <- BEDMatrix(path)

# Get the dimensions of the BEDMatrix object
dim(m)

# Get the row names of the BEDMatrix object
rownames(m)

# Get the column names of the BEDMatrix object
colnames(m)

# Extract genotypes for the specified sample(s)
m[1, ]
m[1:3, ]
m["per0_per0", ]
m[c("per0_per0", "per1_per1", "per2_per2"), ]

# Extract genotypes for a particular variant
m[, 1]
m[, c("snp0_A", "snp1_C", "snp2_G")]

# Extract genotypes for the specified samples and variants
m[
    c("per0_per0", "per1_per1", "per2_per2"),
    c("snp0_A", "snp1_C", "snp2_G")
]

BEDMatrix

Extract Genotypes from a PLINK .bed File

v2.0.3

MIT + file LICENSE

Authors

Alexander Grueneberg [aut, cre], Gustavo de los Campos [ctb]

Initial release