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 = TRUE,
        verbose = FALSE,
        na_noise = FALSE,
        bin = 1,
        threshold = 0,
        cross_width = 200,
        wSize = 10000,
        kernel_width = 1000,
        outLC = FALSE,
        LCScale = "LOG",
        LC_FDR = 0.5
    )

### 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 TRUE
`verbose` | Provides a verbose output when Stereogene is run. Equivalent to -v or -verbose argument in StereoGene.Default FALSE
`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
`outLC` | Write local kerneled correlations into a bedgraph file. Default FALSE.
`LCScale` | Local correlation scale: logarithmic ("LOG") or linear ("LIN") scaling. Default "LOG".
`LC_FDR` | Threshold for local kernel correlation FDR to be written into the local correlation file. Default 0.5

### 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 1.0.0 Index]