runStereogeneOnCapR: runStereogeneOnCapR

In nearBynding: Discern RNA structure proximal to protein binding

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,
    ...
)

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

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")

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