| Title: | Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation. |
|---|---|
| Description: | Datasets to support COPDSexaulDimorphism Package. |
| Authors: | J Fah Sathirapongsasuti |
| Maintainer: | J Fah Sathirapongsasuti <[email protected]> |
| License: | LGPL-2.1 |
| Version: | 1.48.0 |
| Built: | 2026-10-13 13:33:27 UTC |
| Source: | https://github.com/bioc/COPDSexualDimorphism.data |
Data package to accompany the Package COPDSexualDimorphism.
| Package: | COPDSexualDimorphism.data |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2013-10-14 |
| License: | LGPL-2.1 |
Along with the method package COPDSexualDimorphism, this data package is to accompany the paper "Integrative Genomics of Sexual Dimorphism in COPD" by Sathirapongsasuti et al.
J Fah Sathirapongsasuti
Maintainer: J Fah Sathirapongsasuti <[email protected]>
Sathirapongsasuti JF, Glass K, Huttenhower C, Quackenbush J, DeMeo DL. Integrative Genomics of Sexual Dimorphism in COPD. (In Prep).
www.lung-genomics.org
data(lgrc.expr.meta) data(lgrc.expr) data(lgrc.genes)data(lgrc.expr.meta) data(lgrc.expr) data(lgrc.genes)
Gene expression and methylation data from the Lung Genomics Research Consortium.
These are from whole lungs of patients with and without COPD.
Preprocessing, normalization, batch effect correction, and quality control steps
are described in Sathirapongsasuti et al. Three types of data are available:
gene expression (lgrc.expr and lgrc.expr.meta), methylation (lgrc.methp),
and eQTL (lgrc.eqtl).
lgrc.genes are the information about genes in lgrc.expr as given by BiomaRt.
The data frame eqtl is a result of eQTL analysis of cis SNPs within
100kb upstream and 10kb downstream of the SDCD genes. It is the full list of
eQTL results and are to be filtered further through sdcd.core function
as shown in the vignette.
data(lgrc.expr)data(lgrc.expr)
The format is: num [1:14557, 1:229] 10.45 1.88 12 9.02 8.81 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:14557] "ENSG00000000003" "ENSG00000000005" "ENSG00000000419" "ENSG00000000457" ... ..$ : chr [1:229] "LT001098RU_COPD" "LT001796RU_CTRL" "LT005419RU_COPD" "LT007392RU_COPD" ...
www.lung-genomics.org
Sathirapongsasuti JF, Glass K, Huttenhower C, Quackenbush J, DeMeo DL. Integrative Genomics of Sexual Dimorphism in COPD. (In Prep).
data(lgrc.meta) head(meta) data(lgrc.expr) data(lgrc.expr.meta) dim(expr) dim(expr.meta) head(expr.meta) data(lgrc.methp) dim(methp) data(lgrc.eqtl) dim(eqtl)data(lgrc.meta) head(meta) data(lgrc.expr) data(lgrc.expr.meta) dim(expr) dim(expr.meta) head(expr.meta) data(lgrc.methp) dim(methp) data(lgrc.eqtl) dim(eqtl)