runStereogene: runStereogene
In nearBynding: Discern RNA structure proximal to protein binding

Description Usage Arguments Value Examples

Writes a StereoGene script in the working directory

1	runStereogene(track_files, name_config, pcorProfile = NULL, confounder = NULL)

`track_files`	Vector of at least two track or interval file names to be pairwise-correlated by StereoGene. Required.
`name_config`	Name of corresponding configuration file; a string. Required
`pcorProfile`	Name of track file name for partial correlation; a string. More information for this can be found in the StereoGene README. Optional
`confounder`	Confounder file name; a string. More information for this can be found in the StereoGene README. Optional

generates StereoGene output files in directory

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runStereogene(track_files = c("chr4and5_3UTR_stem_liftOver.bedGraph",
                                "chr4and5_liftOver.bedGraph"),
                name_config = "chr4and5_3UTR.cfg")