symmetryContext {nearBynding} | R Documentation

## symmetryContext

### Description

Calculate the symmetry of a binding context.

### Usage

    symmetryContext(
      dir_stereogene_output = ".",
      context_file,
      protein_file,
      protein_file_input = NULL,
      range = c(-200, 200)
    )

### Arguments

`dir_stereogene_output` | Directory of Stereogene output for protein. Default current directory.
`context_file` | Name of the RNA context file input to Stereogene. File names must exclude extensions such as ".bedGraph". Requred
`protein_file` | A vector of at least one protein file name to be averaged for calculation of distance. File names must exclude extensions such as ".bedGraph". All files in the list should be experimental/biological replicates. Required.
`protein_file_input` | A protein file name of background input to be subtracted from protein_file signal. File name must exclude extension. Only one input file is permitted. Optional.
`range` | A vector of two integers denoting the range upstream and downstream of the center of protein binding to consider in the comparison. Ranges that are too small miss the holistic binding context, while large ranges amplify distal noise in the binding data. Cannot exceed wSize/2 from write_config. Default c(-200, 200)

### Value

Wasserstein distance between the two halves of the binding context, with lower values suggesting greater symmetry.

### Examples

    ## load example StereoGene output
    get_outfiles()

    ## This boring example compares a protein's binding with itself for all
    ## contexts, therefore the distance is 0
    symmetryContext(context_file = "chr4and5_3UTR_stem_liftOver",
                           protein_file = "chr4and5_liftOver")

[Package nearBynding version 1.4.0 Index]