# PlinkMatrix: DelayedArray interface for plink genotypes
Given a collection of .bed, .bim and .fam files produced
for use with Plink, this package facilitates simple
array-like operations for retrieving genotype data.
## Installation
Use Bioconductor 3.23.
```
BiocManager::install("PlinkMatrix")
```
## Example
As an example, the GEUVADIS study genotypes distributed
with tensorQTL were transformed to `geuv445.{bed,bim,fam}`.
In a folder containing these files, we would proceed
as follows to interrogate the genotypes.
```
> library(PlinkMatrix)
> gdemo = example_PlinkMatrix()
> colnames(gdemo) = gsub("0_", "", colnames(gdemo))
> gdemo
<367759 x 445> DelayedMatrix object of type "double":
HG00096 HG00097 HG00099 ... NA20826 NA20828
chr18_10644_C_G_b38 0 0 0 . 0 0
chr18_10847_C_A_b38 0 0 0 . 0 0
chr18_11275_G_A_b38 0 0 0 . 0 0
chr18_11358_G_A_b38 0 0 0 . 0 0
chr18_11445_G_A_b38 0 0 0 . 0 0
... . . . . . .
chr18_80259028_AG_A_b38 1 2 2 . 0 1
chr18_80259147_G_C_b38 0 0 0 . 0 0
chr18_80259181_A_G_b38 0 0 0 . 0 0
chr18_8025919C_G_b38 1 0 0 . 1 0
chr18_80259245_C_A_b38 0 0 0 . 0 0
```
The associated data can be obtained in this package with `example_PlinkMatrix()`.
See "Get started" tab above for more information.
