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

View on CRAN

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