bed-class: Class bed
In bigsnpr: Analysis of Massive SNP Arrays
bed-class R Documentation
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
bedfile <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
(obj.bed <- bed(bedfile))
bigsnpr documentation built on March 31, 2023, 10:37 p.m.
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| bed-class | R Documentation |
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 aXPtr<bed>in C++ code -
$extptr: use$addressinstead -
$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 -
$.map: use$mapinstead -
$.fam: use$faminstead -
$light: get a lighter version of this object for parallel algorithms to not have to transfer e.g.$.map.
Examples
bedfile <- system.file("extdata", "example-missing.bed", package = "bigsnpr")
(obj.bed <- bed(bedfile))
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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