bindingContextDistanceCapR: bindingContextDistanceCapR

In nearBynding: Discern RNA structure proximal to protein binding

Description

Calculate the Wasserstein distance between two replicates' or two proteins' binding contexts.

Usage

bindingContextDistanceCapR(
    dir_stereogene_output = ".",
    CapR_prefix = "",
    protein_file,
    protein_file_input = NULL,
    dir_stereogene_output_2 = NULL,
    CapR_prefix_2 = "",
    protein_file_2,
    protein_file_input_2 = NULL,
    context = "all",
    range = c(-200, 200)
)

Arguments

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.
dir_stereogene_output_2	Directory of Stereogene output for second protein. Default current directory.
CapR_prefix_2	The prefix common to CapR output files of protein_file_2, if applicable.Equivalent to output_prefix from r unStereogeneOnCapR. Default ""
protein_file_2	Similar to protein_file. A second 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_2	Similar to protein_file_input. A second protein file name of background input to be subtracted from protein_file_2 signal. File name must exclude extension. Only one input file is permitted. Optional.
context	The RNA structure context being compared for the two protein file sets. 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)

Value

Wasserstein distance between the two protein file sets provided for the RNA structure context specified, minus the input binding signal if applicable

Note

Wasserstein distance calculations are reciprocal, so it does not matter which protein is first or second so long as replicates and input files correspond to one another.

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
bindingContextDistanceCapR(CapR_prefix = "chr4and5_3UTR",
                            protein_file = "chr4and5_liftOver",
                            CapR_prefix_2 = "chr4and5_3UTR",
                            protein_file_2 = "chr4and5_liftOver")

nearBynding documentation built on Nov. 8, 2020, 8:15 p.m.