RaMWAS: Fast Methylome-wide Association Study Pipeline for Enrichment...
In andreyshabalin/ramwas: Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Description
Details
Author(s)
See Also
Description
RaMWAS provides a complete toolset for
methylome-wide association studies (MWAS).
It is specifically designed for data from
enrichment based methylation assays,
but can be applied to other methylomic data as well.
The analysis pipeline includes seven steps:
(1) scanning aligned reads from BAM files,
(2) calculation of quality control measures,
(3) creation of methylation score (coverage) matrix,
(4) principal component analysis for capturing batch effects and
detection of outliers,
(5) association analysis with respect to phenotypes of interest
while correctingfor top PCs and known covariates,
(6) annotation of significant findings, and
(7) multi-marker analysis (methylation risk score) using elastic net.
Details
Package: ramwas
Type: Package
License: LGPL-3
LazyLoad: yes
Depends: methods
Author(s)
Andrey A Shabalin andrey.shabalin@gmail.com
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
See Also
See vignettes: browseVignettes("ramwas").
andreyshabalin/ramwas documentation built on Sept. 27, 2021, 7:25 p.m.
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Description Details Author(s) See Also
Description
RaMWAS provides a complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other methylomic data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correctingfor top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net.
Details
| Package: | ramwas |
| Type: | Package |
| License: | LGPL-3 |
| LazyLoad: | yes |
| Depends: | methods |
Author(s)
Andrey A Shabalin andrey.shabalin@gmail.com
Maintainer: Andrey A Shabalin <andrey.shabalin@gmail.com>
See Also
See vignettes: browseVignettes("ramwas").
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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