runCapR: runCapR
In nearBynding: Discern RNA structure proximal to protein binding

Description Usage Arguments Value Examples

Runs CapR

1	runCapR(in_file, out_file = NA, max_dist = 100)

`in_file`	An .fa file like from ExtractTranscriptomeSequence that is a list of fasta sequences to be folded. Required
`out_file`	Name of the CapR output file of nucleotide folding probabilities. Default is in_file prefix.out
`max_dist`	Integer of maximum distance between folded nucleotides in sequences. Recommeded between 50 and 100, with higher values yielding potentially more accurate results but dramatically increasing run time. Default 100.

generates CapR outfile

## make dummy file
write_fasta(paste0(sample(c("A", "T", "G", "C"), 50, replace = TRUE),
                    collapse = ""),
            "test",
            "test.fa")
## run CapR
runCapR("test.fa")