epic: Run pre-defiend scripts

In eilslabs/epic: Integrative Analysis and Visualization of Epigenomic Sequencing Data

Description

Run pre-defiend scripts

Usage

epic()

Details

There are some R scripts which can be run directly. The path of all scripts can be obtained by

   dir(system.file("pipeline", "script", package = "epic"), pattern = "\.R$")  

You can either directly run these R scripts by:

   Rscript full-path-of-cmd.R [options]  

or use the short command:

   Rscript -e "epic::epic()" cmd [options]  

For each cmd, use Rscript -e "epic::epic()" cmd --help to get help.

Basically all scripts need --config option which corresponds to a configuration R file that defines how to get data.

Available commands (cmd) are:

chromatin_states_transitions

visualize chromatin states transitions by chord diagram

correlated_enriched

visualize enrichment of correlated regions on tss/cgi/tfbs/enhancers

correlated_regions

find regions in which methylation is correlated to expression of the associated gene

correlated_regions_downstream

visualize statistics of correlated regions, visualize genome-wide distribution of correlated regions by Hilbert curve

correlated_regions_filter

only keep correlation regions with significant correlations. Subgroup specificity for each class is calculated if needed.

correlated_regions_gviz

visualize correlated regions and other associated information by Gviz package

correlated_regions_reduce

reduce correlated regions

differential_methylation_in_cgi_and_shore

visualize differentially methylated regions in cgi and shores

differential_methylation_in_genomic_features

visualize differentially methylated regions in a set of genomic features.

general_methylation_distribution

use heatmap to visualize methylation distribution

methylation_subtype_classification_in_cgi_and_shore

classify subgroups by methylation in cgi and shores

Value

No value is returned.

Author(s)

Zuguang Gu <[e-mail]>

Examples

# There is no example
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eilslabs/epic documentation built on May 16, 2019, 1:24 a.m.