Read the GRM binary file.

Description

Function provided by GCTA maintainers (modified slightly) for accessing their recently introduced binary GRM format. The GRM is stored as a vector of numerics which correspond to the lower triangular elements including the diagonal. We simply read these, pull the diagonal elements, and inflate them into a full symmetric matrix. We add sample IDs to colnames and rownames for compatibility with other Kriging functions.

Usage

read_GRMBin(prefix, size = 4)

Arguments

Details

Note that the GRM is described by three files, and this function assumes that all have a common prefix that is passed in.

Value

GRM of dim (N.samples x N.samples) with rownames and colnames as sample ID.

References

http://www.complextraitgenomics.com/software/gcta/estimate_grm.html

Examples

  ## read binary Genetic Relatedness Matrix (GRM) generated by GCTA
  grmFile <- system.file(package = "OmicKriging",
                         "doc/vignette_data/ig_genotypes.grm.bin")
  grmFileBase <- substr(grmFile,1, nchar(grmFile) - 4)
  GRM <- read_GRMBin(grmFileBase)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(OmicKriging)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/OmicKriging/read_GRMBin.Rd_%03d_medium.png", width=480, height=480)
> ### Name: read_GRMBin
> ### Title: Read the GRM binary file.
> ### Aliases: read_GRMBin
> 
> ### ** Examples
> 
>   ## read binary Genetic Relatedness Matrix (GRM) generated by GCTA
>   grmFile <- system.file(package = "OmicKriging",
+                          "doc/vignette_data/ig_genotypes.grm.bin")
>   grmFileBase <- substr(grmFile,1, nchar(grmFile) - 4)
>   GRM <- read_GRMBin(grmFileBase)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>