runCapR: runCapR

Description Usage Arguments Value Examples

View source: R/runCapR.R

Description

Runs CapR

Usage

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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

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

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