runCapR {nearBynding} | R Documentation |
Runs CapR
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")