write_config: write_config
In nearBynding: Discern RNA structure proximal to protein binding

Description Usage Arguments Value Note Examples

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

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
)

`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

writes a configuration file into directory

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.

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