README.md

In QuantGen/grmMatrix: Matrices Backed by Binary GRM Files (GCTA)

grmMatrix

Example

This example uses dummy GRM files bundled with this package. It was generated from the dummy BED files in the BEDMatrix package 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):

> prefix <- paste0(system.file("extdata", package = "grmMatrix"), "/example")

To wrap the dummy GRM files in a grmMatrix object:

> m <- grmMatrix$new(prefix = prefix)

To get the dimensions of the grmMatrix object:

> dim(m)
[1] 50 50

To extract a subset of the BEDMatrix object:

> 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:

> 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:

# install.packages("devtools")
devtools::install_github("QuantGen/grmMatrix")

QuantGen/grmMatrix documentation built on May 8, 2019, 3:51 a.m.