https://github.com/quantgen/grmmatrix
https://github.com/quantgen/grmmatrix
r r-pkg
Last synced: 16 days ago
JSON representation
- Host: GitHub
- URL: https://github.com/quantgen/grmmatrix
- Owner: QuantGen
- License: other
- Created: 2017-01-26T18:43:52.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2017-02-24T20:20:46.000Z (over 9 years ago)
- Last Synced: 2025-10-25T23:44:03.786Z (9 months ago)
- Topics: r, r-pkg
- Language: R
- Size: 13.7 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
grmMatrix
=========
[](https://travis-ci.org/QuantGen/grmMatrix)
[](https://cran.r-project.org/package=grmMatrix)
[](http://www.rdocumentation.org/packages/grmMatrix)
Example
-------
This example uses dummy GRM files bundled with this package. It was generated from the dummy BED files in the [BEDMatrix package](https://cran.r-project.org/package=BEDMatrix) using `gcta64 --bfile example --make-grm --out example` with GCTA 1.26.0.
To get the prefix to the dummy GRM files (`system.file` finds the full file names of files in packages and is only used to find the example data):
```r
> prefix <- paste0(system.file("extdata", package = "grmMatrix"), "/example")
```
To wrap the dummy GRM files in a grmMatrix object:
```r
> m <- grmMatrix$new(prefix = prefix)
```
To get the dimensions of the grmMatrix object:
```r
> dim(m)
[1] 50 50
```
To extract a subset of the BEDMatrix object:
```r
> m[1:3, 1:3]
per0_per0 per1_per1 per2_per2
per0_per0 0.99297035 0.045664247 0.956165433
per1_per1 0.04566425 0.956165433 -0.003567911
per2_per2 0.95616543 -0.003567911 0.981300116
```
To extract the diagonal of the grmMatrix object:
```r
> diag(m)
per0_per0 per1_per1 per2_per2 per3_per3 per4_per4 per5_per5
0.9929703 0.9561654 0.9813001 1.0006099 0.9571444 1.0086495
per6_per6 per7_per7 per8_per8 per9_per9 per10_per10 per11_per11
0.9779904 0.9986514 0.9818304 1.0304354 0.9246207 0.9786042
per12_per12 per13_per13 per14_per14 per15_per15 per16_per16 per17_per17
1.0067449 0.9791979 1.0073903 0.9919306 0.9969872 1.0002682
per18_per18 per19_per19 per20_per20 per21_per21 per22_per22 per23_per23
1.0341240 1.0021822 0.9916793 0.9868485 1.0195130 1.0006720
per24_per24 per25_per25 per26_per26 per27_per27 per28_per28 per29_per29
1.0005078 1.0038743 0.9981703 1.0563536 1.0256737 0.9853888
per30_per30 per31_per31 per32_per32 per33_per33 per34_per34 per35_per35
0.9726509 1.0062875 1.0499943 1.0089763 1.0286126 0.9993057
per36_per36 per37_per37 per38_per38 per39_per39 per40_per40 per41_per41
1.0158972 1.0061988 0.9454290 0.9622741 1.0020869 0.9885394
per42_per42 per43_per43 per44_per44 per45_per45 per46_per46 per47_per47
1.0198814 0.9933779 1.0055650 1.0098705 0.9839650 1.0303550
per48_per48 per49_per49
1.0059229 0.9897712
```
Installation
------------
To get the current development version from GitHub:
```r
# install.packages("devtools")
devtools::install_github("QuantGen/grmMatrix")
```