Description Usage Arguments Value References Examples

View source: R/correlation_matrices.R

Function to write a binary GRM format recently introduced by GCTA. It takes a correlation matrix as used by other Kriging functions, and writes three files: binary file for storing the diagonal + lower triangular elements, a text file for sample IDs, and a binary file storing the number of SNPs used in the correlation matrix calculation.

1 | ```
write_GRMBin(X, n.snps = 0, prefix, size = 4)
``` |

`X` |
Correlation matrix with rownames and colnames as sample IDs. |

`n.snps` |
Number of SNPs used in correlation matrix calculation. Default is 0.0. |

`prefix` |
Base file path and names for the three output files. |

`size` |
Number of bytes to write for each value. Default is 4 |

None. Though side effects are writing three files as described above.

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

1 2 3 4 5 6 7 8 9 10 | ```
## create a random genotype matrix
nSamples <- 10
mMarkers <- 100
X <- matrix(rbinom(n=100, size=2, prob=0.5), nrow=nSamples)
## compute the Genetric Relatedness Matrix
grm <- cor(X)
## write a Genetic Relatedness Matrix (GRM)
## NOTE: to following is not run here -- not writing any files in examples
#write_GRMBin(grm, n.snps=mMarkers, prefix="grm.out")
``` |

OmicKriging documentation built on May 19, 2017, 9:53 a.m.

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