grsExample: Filtered Mock Epigenomics Data Set
In nhejazi/methyvimData: Example experimental data for use with the methyvim package
Description
Usage
Format
Details
Value
Examples
Description
A data set containing data that is similar in structure to that typically
found in epigenomics studies.
Usage
1
Format
An object of class GenomicRatioSet with 400 rows and 210 columns.
Details
This data set was simulated based on several key characteristics of data
sets available to the package authors through collaborations in studies of
differential methylation. It is based on data collected using the 850K
(EPIC) Infinium arrays produced by Illumina, from samples collected on
human subjects in studies of environmental epidemiology. The structure of
the original data set (e.g., notable differences between the exposure and
treatment conditions) were used to guide the simulation, and data was only
produced for an arbitrary subset of sites. The phenotype-level exposure and
outcome data (accessible via colData) were derived from the original
data. The size of the subset was chosen such that the data package would be
compliant with the standards outlined by Bioconductor. We emphasize that
this is not real data and is not in any way suitable for scientific
investigation. Please note that THIS IS NOT REAL DATA.
Value
A GenomicRatioSet containing pre-filtered CpG sites, ready to
be used with the core function of the methyvim package.
Examples
1
2
3
4
5
6
7
# Load required packages and the data set
suppressMessages(library(SummarizedExperiment))
data(grsExample)
# Take a look at the data in the GenomicRatioSet object
grsExample
# Extract treatment/exposure values with colData
as.numeric(colData(grsExample)[, 1])
nhejazi/methyvimData documentation built on May 30, 2019, 7:17 p.m.
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Description Usage Format Details Value Examples
Description
A data set containing data that is similar in structure to that typically found in epigenomics studies.
Usage
1 |
Format
An object of class GenomicRatioSet with 400 rows and 210 columns.
Details
This data set was simulated based on several key characteristics of data
sets available to the package authors through collaborations in studies of
differential methylation. It is based on data collected using the 850K
(EPIC) Infinium arrays produced by Illumina, from samples collected on
human subjects in studies of environmental epidemiology. The structure of
the original data set (e.g., notable differences between the exposure and
treatment conditions) were used to guide the simulation, and data was only
produced for an arbitrary subset of sites. The phenotype-level exposure and
outcome data (accessible via colData) were derived from the original
data. The size of the subset was chosen such that the data package would be
compliant with the standards outlined by Bioconductor. We emphasize that
this is not real data and is not in any way suitable for scientific
investigation. Please note that THIS IS NOT REAL DATA.
Value
A GenomicRatioSet containing pre-filtered CpG sites, ready to
be used with the core function of the methyvim package.
Examples
1 2 3 4 5 6 7 | # Load required packages and the data set
suppressMessages(library(SummarizedExperiment))
data(grsExample)
# Take a look at the data in the GenomicRatioSet object
grsExample
# Extract treatment/exposure values with colData
as.numeric(colData(grsExample)[, 1])
|
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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