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 |

**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.

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
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