bigsnpr (version 1.6.1)

bed-class: Class bed

Description

A reference class for storing a pointer to a mapped version of a bed file.

Usage

bed(bedfile)

Arguments

bedfile

Path to file with extension ".bed" to read. You need the corresponding ".bim" and ".fam" in the same directory.

Details

A bed object has many field:

• $address: address of the external pointer containing the underlying C++ object, to be used internally as a XPtr<bed> in C++ code

• $extptr: use $address instead

• $bedfile: path to the bed file

• $bimfile: path to the corresponding bim file

• $famfile: path to the corresponding fam file

• $prefix: path without extension

• $nrow: number of samples in the bed file

• $ncol: number of variants in the bed file

• $map: data frame read from $bimfile

• $fam: data frame read from $famfile

• $.map: use $map instead

• $.fam: use $fam instead

• $light: get a lighter version of this object for parallel algorithms to not have to transfer e.g. $.map.

Examples

# NOT RUN {
bedfile <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
(obj.bed <- bed(bedfile))

# }