runStereogeneOnCapR: runStereogeneOnCapR

In vbusa1/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,
  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")

vbusa1/nearBynding documentation built on Aug. 4, 2021, 4:08 p.m.