In bulk epigenome/transcriptome experiments, molecular expression is measured in a tissue, which is a mixture of multiple types of cells. This package tests association of a disease/phenotype with a molecular marker for each cell type. The proportion of cell types in each sample needs to be given as input. The package is applicable to epigenome-wide association study (EWAS) of microarray experiments. Takeuchi and Kato (submitted) "omicwas: cell-type-specific epigenome-wide and transcriptome association study".
Version: | 0.3.1 |
Depends: | R (≥ 3.6.0) |
Imports: | broom, data.table, dplyr, ff, glmnet, magrittr, MASS, matrixStats, parallel, PCDimension, ridge, rlang, R.utils, sva, tidyr |
Suggests: | testthat |
Published: | 2020-02-19 |
Author: | Fumihiko Takeuchi |
Maintainer: | Fumihiko Takeuchi <fumihiko at takeuchi.name> |
BugReports: | https://github.com/fumi-github/omicwas/issues |
License: | GPL-3 |
URL: | https://github.com/fumi-github/omicwas |
NeedsCompilation: | no |
Materials: | README |
CRAN checks: | omicwas results |
Reference manual: | omicwas.pdf |
Package source: | omicwas_0.3.1.tar.gz |
Windows binaries: | r-prerelease: omicwas_0.3.1.zip, r-release: omicwas_0.3.1.zip, r-oldrel: not available |
macOS binaries: | r-prerelease: not available, r-release: omicwas_0.3.1.tgz, r-oldrel: not available |
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