HextractoR: HextractoR: Integrated Tool for Hairping Extraction of RNA...
In HextractoR: Integrated Tool for Hairping Extraction of RNA Sequences

Description Usage Arguments Value Examples

View source: R/HextractoR.R

To preprocess a genome, you need a file containing the raw genome in fasta format. To run HExtractor, simply call the main function. This function creates 2 files in the "out" folder and automatically names them.

HextractoR(input_file, min_valid_nucleotides = 500, window_size = 160,
  window_step = 30, only_sloop = T, min_length = 60, min_bp = 16,
  trim_sequences = T, margin_bp = 6, blast_evalue = 1,
  identity_threshold = 90, nthreads = 4, nworks = 4,
  filter_files = { })

`input_file`	filename of the fasta file to proccess
`min_valid_nucleotides`	Each input sequence must have this quantity of valid nucleotides (not 'N') to be processed.
`window_size`	Number of bases in the windows.
`window_step`	Window step. This number defines indirectly the overlap: window_overlap=window_size-window_step
`only_sloop`	Only extract single loop sequence.
`min_length`	Minimum sequence length. Shorter sequences are discarded.
`min_bp`	Minimum number of base-pairs that must form a sequence.
`trim_sequences`	Use some heuristics to trim the hairpins.
`margin_bp`	When the sequence is trimmed, at least min_bp+margin_bp base-pairs are left.
`blast_evalue`	e-value used in blast to match the extracted sequences with the sequences from the filter files.
`identity_threshold`	Identity threshold used to match sequences with the sequences from the filter files.
`nthreads`	Allows using more than one thread in the execution.
`nworks`	Split each sequence in nworks to use less RAM memory.
`filter_files`	Fasta files with known sequences to separate the output stems.

A list with the path of the output files and the result of the proccessing of each sequence (if it was succesful or failed)

# Small example without filter files
library(HextractoR)
# First we get the path of the example FASTA file
fpath <- system.file("Example_tiny.fasta", package="HextractoR")
# To run HextractoR, simply call the main function
HextractoR(input_file = fpath)
# Other example with filter files and bigger input file
fpath1 <- system.file("Example_human.fasta", package="HextractoR")
fpath2 <- system.file("Example_pre-miRNA.fasta", package="HextractoR")
HextractoR(input_file = fpath1, filter_files = {fpath2})
# This function creates 2 files in the working directory and automatically
# names them.