runStereogene {nearBynding} | R Documentation |
Writes a StereoGene script in the working directory
runStereogene(track_files, name_config, pcorProfile = NULL, confounder = NULL, nShuffle = 1000, get_error = FALSE)
track_files |
Vector of at least two track or interval file names to be pairwise-correlated by StereoGene. Required. |
name_config |
Name of corresponding configuration file; a string. Required |
pcorProfile |
Name of track file name for partial correlation; a string. More information for this can be found in the StereoGene README. Optional |
confounder |
Confounder file name; a string. More information for this can be found in the StereoGene README. Optional |
nShuffle |
Permutations used to estimate error. Default 5000. |
get_error |
Whether to calculate the standard error of background permutations from nShuffle. FALSE will save calculation time. Default FALSE |
generates StereoGene output files in directory
runStereogene(track_files = c("chr4and5_3UTR_stem_liftOver.bedGraph", "chr4and5_liftOver.bedGraph"), name_config = "chr4and5_3UTR.cfg")