runStereogeneOnCapR {nearBynding} | R Documentation

## runStereogeneOnCapR

### Description

Writes a configuration file and Stereogene script and runs Stereogene for all CapR tracks

### Usage

    runStereogeneOnCapR(
      dir_CapR_bg = ".",
      input_prefix,
      protein_file,
      output_prefix = input_prefix,
      name_config = "config.cfg",
      chrom_size,
      nShuffle = 100,
      get_error = FALSE,
      ...
    )

### Arguments

`dir_CapR_bg` | Directory of lifted-over CapR bedGraph files. Default current directory
`input_prefix` | Prefix string appended to input files; same as input_prefix argument in processCapRout. Required
`protein_file` | Name of protein file in bedGraph format. Required
`output_prefix` | Prefix string to be appended to all output files. Default to be same as input_prefix
`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
`...` | includes all other parameters acceptable to write_config and write_stereogene
`nShuffle` | Permutations used to estimate error. Default 100.
`get_error` | Whether to calculate the standard error of background permutations from nShuffle. FALSE will save calculation time. Default FALSE

### Value

generates StereoGene output files, including *.dist files

### Examples

    runStereogeneOnCapR(protein_file = "chr4and5_liftOver.bedGraph",
                       chrom_size = "chr4and5_3UTR.size",
                       name_config = "chr4and5_3UTR.cfg",
                       input_prefix = "chr4and5_3UTR")

[Package nearBynding version 1.4.0 Index]