# OmicKriging: Poly-Omic Prediction of Complex TRaits

It provides functions to generate a correlation matrix from a genetic dataset and to use this matrix to predict the phenotype of an individual by using the phenotypes of the remaining individuals through kriging. Kriging is a geostatistical method for optimal prediction or best unbiased linear prediction. It consists of predicting the value of a variable at an unobserved location as a weighted sum of the variable at observed locations. Intuitively, it works as a reverse linear regression: instead of computing correlation (univariate regression coefficients are simply scaled correlation) between a dependent variable Y and independent variables X, it uses known correlation between X and Y to predict Y.

- Author
- Hae Kyung Im, Heather E. Wheeler, Keston Aquino Michaels, Vassily Trubetskoy
- Date of publication
- 2016-03-08 00:12:43
- Maintainer
- Hae Kyung Im <haky@uchicago.edu>
- License
- GPL (>= 3)
- Version
- 1.4.0

## Man pages

- krigr_cross_validation
- Multithreaded cross validation routine for Omic Kriging.
- load_sample_data
- Loads sample phenotype and covariate data into data frame.
- make_GXM
- Compute gene expression correlation matrix.
- make_PCs_irlba
- Run Principal Component Analysis (PCA) using the irlba...
- make_PCs_svd
- Run Principal Component Analysis (PCA) using base R svd()...
- okriging
- Run omic kriging on a set of correlation matrices and a given...
- read_GRMBin
- Read the GRM binary file.
- write_GRMBin
- Write GRM binary files.

## Files in this package

OmicKriging |

OmicKriging/inst |

OmicKriging/inst/doc |

OmicKriging/inst/doc/OmicKriging.R |

OmicKriging/inst/doc/vignette_data |

OmicKriging/inst/doc/vignette_data/ig_genotypes.bed |

OmicKriging/inst/doc/vignette_data/ig_genotypes.grm.id |

OmicKriging/inst/doc/vignette_data/ig_genotypes.fam |

OmicKriging/inst/doc/vignette_data/ig_genotypes.grm.N.bin |

OmicKriging/inst/doc/vignette_data/ig_genotypes.bim |

OmicKriging/inst/doc/vignette_data/ig_pheno.txt |

OmicKriging/inst/doc/vignette_data/ig_genotypes.grm.bin |

OmicKriging/inst/doc/vignette_data/ig_gene_subset.txt.gz |

OmicKriging/inst/doc/OmicKriging.Rnw |

OmicKriging/inst/doc/OmicKriging.pdf |

OmicKriging/NAMESPACE |

OmicKriging/R |

OmicKriging/R/omic_KRIGR.R |

OmicKriging/R/input_pheno_GT.R |

OmicKriging/R/correlation_matrices.R |

OmicKriging/vignettes |

OmicKriging/vignettes/vignette_data |

OmicKriging/vignettes/vignette_data/ig_genotypes.bed |

OmicKriging/vignettes/vignette_data/ig_genotypes.grm.id |

OmicKriging/vignettes/vignette_data/ig_genotypes.fam |

OmicKriging/vignettes/vignette_data/ig_genotypes.grm.N.bin |

OmicKriging/vignettes/vignette_data/ig_genotypes.bim |

OmicKriging/vignettes/vignette_data/ig_pheno.txt |

OmicKriging/vignettes/vignette_data/ig_genotypes.grm.bin |

OmicKriging/vignettes/vignette_data/ig_gene_subset.txt.gz |

OmicKriging/vignettes/OmicKriging.Rnw |

OmicKriging/README.md |

OmicKriging/MD5 |

OmicKriging/build |

OmicKriging/build/vignette.rds |

OmicKriging/DESCRIPTION |

OmicKriging/man |

OmicKriging/man/write_GRMBin.Rd |

OmicKriging/man/okriging.Rd |

OmicKriging/man/make_GXM.Rd |

OmicKriging/man/make_PCs_irlba.Rd |

OmicKriging/man/load_sample_data.Rd |

OmicKriging/man/krigr_cross_validation.Rd |

OmicKriging/man/read_GRMBin.Rd |

OmicKriging/man/make_PCs_svd.Rd |