runStereogene: runStereogene
In vbusa1/nearBynding: Discern RNA structure proximal to protein binding

Description Usage Arguments Value Examples

Writes a StereoGene script in the working directory

runStereogene(track_files,
        name_config,
        pcorProfile = NULL,
        confounder = NULL,
        nShuffle = 1000,
        get_error = FALSE)

`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
`nShuffle`	Permutations used to estimate error. Default 5000.
`get_error`	Whether to calculate the standard error of background permutations from nShuffle. FALSE will save calculation time. Default FALSE

generates StereoGene output files in directory

1
2
3

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