runCapR {nearBynding} | R Documentation

## runCapR

### Description

Runs CapR

### Usage

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

### Arguments

`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.

### Value

generates CapR outfile

### Examples

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

[Package nearBynding version 1.0.0 Index]