epik: Run pre-defiend scripts
In jokergoo/epik.cmd: Run epik analysis under command line

Description Usage Details Value Author(s) Examples

View source: R/epik.R

Run pre-defiend scripts

epik()

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

1	dir(system.file("pipeline", "scripts", package = "epik.cmd"), pattern = "\.R$")

You can either directly run these R scripts by:

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

or use the short command:

1	Rscript -e "epik.cmd::epik()" cmd [options]

to get the list of commands:

1	Rscript -e "epikc.cmd::epik()"

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

Basically all scripts need --config option which corresponds to a configuration R file that defines how to import data. A template for the configuration file is at:

1	system.file("pipeline", "pipeline_configure_template.R", package = "epik.cmd")

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