This package provides commands for running specific analysis from epik package under command-line mode.
To see commands which are supported:
~/project\> Rscript -e "epik.cmd::epik()"
Usage: Rscript -e "epik.cmd::epik()" cmd [options]
Available cmd:
chromatin_states_transitions
correlated_regions
cr_add_fdr
cr_enriched_heatmap
cr_genic_stat
cr_global_vis
cr_gviz
cr_reduce
cr_scatterplot
cr_sig_heatmap
diff_meth_in_cgi_and_shore
diff_meth_in_genomic_features
general_methylation
hc_difference
For each cmd, use 'Rscript -e "epik.cmd::epik()" cmd --help' to get help.
For each command, --help
option prints the help message. E.g:
~/project\> Rscript -e "epik.cmd::epik()" chromatin_states_transitions --help
Visualize chromatin states transitions in two subgroups
Usage: Rscript -e "epik.cmd::epik()" chromatin_states_transitions [options]
--config character
A configuration R script. Check the help page of `load_config()` function to
find out how to properly set one.
--min1 numeric
If there are multiple samples in the group 1, it is possible that a segment has
more than one states asigned to it. If the recurrency of each state is
relatively low, it means there is no one dominant state for this segment and it
should be removed. This argument controls the minimal value for the
recurrency of states in a given segment. The value is a percent. (0.5 by
default)
--min2 numeric
Same as `min1`, but for samples in group 2. (0.5 by default)
--methdiff numeric
The segments for which the methylation difference between two groups is less
than this value are removed. (0 by default)
--equalscale
When there are more than one comparisons, should all chord diagrams have same
scale? (TRUE by default)
--help
Print help message and exit.
--version
Print version information and exit.
To successfully run it, `chipseq_hooks$chromHMM()` must be set beforehand in
the configuration file.
The orders of chromatin states in the plot can be set by `CHROMATIN_STATES_ORDER`
(a vector of state names) and the color can be set by `CHROMATIN_STATES_COLOR` (a
vector of colors for which names are state names) in the configuration file.
GPL (>= 2)
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