write_config {nearBynding} | R Documentation

## write_config

### Description

Writes a configuration file for use by Stereogenes in the working directory.

### Usage

    write_config(
      name_config = "config.cfg",
      chrom_size,
      Rscript = FALSE,
      silent = TRUE,
      na_noise = FALSE,
      bin = 1,
      threshold = 0,
      cross_width = 200,
      wSize = 10000,
      kernel_width = 1000,
      resPath = "."
    )

### Arguments

`name_config` | Name of output config file. Default config.cfg
`chrom_size` | Name of chromosome size file. File must be in two-column format without a header where first column is chromosome name and second column is chromosome length, as from getChainChrSize. Required
`Rscript` | Write R script for the result presentation. Equivalent to -r argument in StereoGene. Default FALSE
`silent` | Provides an output when Stereogene is run. Equivalent to -s or -silent argument in StereoGene. Default TRUE
`na_noise` | Use NA values as unknown and fill them with noise. Equivalent to -NA argument in StereoGene. Default FALSE
`bin` | Bin size for input averaging; an integer. Default 1
`threshold` | Threshold for input data to remove small values. An integer between 0 and 250. Default 0
`cross_width` | Width of cross-correlation plot output in Rscript; an integer. Default 200.
`wSize` | Window size; an integer. If windows are too small, cross correlations will have a lot of noise; if they are too large, there may be too few windows for robust statistical assessment. Default 10000
`kernel_width` | Kernel span in nucleotides; an integer. Equivalent to KernelSigma invStereoGene. Default 1000
`resPath` | Folder to store results. Default is current directory.

### Value

writes a configuration file into directory

### Note

Not all StereoGene parameters are included in this function so refer to the StereoGene manual and modify the output .cfg file manually if additional parameters are desired.

### Examples

    ## Write a config file named "test.cfg" with chromosome size file "test.size"
    write_config(name_config = "test.cfg",
                chrom_size = "test.size")

[Package nearBynding version 1.4.0 Index]