runStereogeneOnCapR {nearBynding} | R Documentation |
Writes a configuration file and Stereogene script and runs Stereogene for all CapR tracks
runStereogeneOnCapR( dir_CapR_bg = ".", input_prefix, protein_file, output_prefix = input_prefix, name_config = "config.cfg", chrom_size, ... )
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 |
generates StereoGene output files, including *.dist files
runStereogeneOnCapR(protein_file = "chr4and5_liftOver.bedGraph", chrom_size = "chr4and5_3UTR.size", name_config = "chr4and5_3UTR.cfg", input_prefix = "chr4and5_3UTR")