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

Description Usage Arguments Value Examples

Calculate the symmetry of a binding context.

symmetryCapR(
  dir_stereogene_output = ".",
  CapR_prefix = "",
  protein_file,
  protein_file_input = NULL,
  context = "all",
  range = c(-200, 200)
)

`dir_stereogene_output`	Directory of Stereogene output for first protein. Default current directory.
`CapR_prefix`	The prefix common to CapR output files of protein_file, if applicable. Equivalent to output_prefix from runStereogeneOnCapR. Default ""
`protein_file`	A vector of strings with 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.
`context`	The RNA structure context being interrogated. Acceptable contexts include "all", which sums the distance of all six contexts, or any of the contexts individually ("bulge", "hairpin", "stem", "exterior", "multibranch", or "internal"). Default "all"
`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)

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

## load example StereoGene output
get_outfiles()

## This boring example compares a protein's binding with itself for all
## contexts, therefore the distance is 0
symmetryCapR(CapR_prefix = "chr4and5_3UTR",
                protein_file = "chr4and5_liftOver")