runStereogene {nearBynding} | R Documentation

## runStereogene

### Description

Writes a StereoGene script in the working directory

### Usage

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

### Arguments

`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

### Value

generates StereoGene output files in directory

### Examples

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

[Package nearBynding version 1.4.0 Index]