% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/map.generator.lnc.R
\name{map_generator_lnc}
\alias{map_generator_lnc}
\title{Infer orthologous lncRNAs between multiple species}
\usage{
map_generator_lnc(
  query_file,
  subjects_folder,
  output_folder,
  task = "blastn",
  eval = "1E-5",
  ortho_detection = "RBH",
  max.target.seqs = 10000,
  min_qry_coverage_hsp = 30,
  min_qry_perc_identity = 30,
  logical_connective = "AND",
  min_alig_length = NULL,
  comp_cores = 1,
  progress_bar = TRUE,
  sep = ";",
  path = NULL,
  ...
)
}
\arguments{
\item{query_file}{a character string specifying the path to the lncRNAs file of the query organism in \code{fasta} format.}

\item{subjects_folder}{a character string specifying the path to the folder where lncRNAs files in \code{fasta} format of the subject organisms are stored.}

\item{output_folder}{a character string specifying the path to the folder where output orthologous tables should be stored.}

\item{task}{nucleotide search task option. Options are:
\itemize{
\item \code{task = "blastn"} : Standard nucleotide-nucleotide comparisons (default) - Traditional BLASTN requiring an exact match of 11.
\item \code{task = "blastn-short"} : Optimized nucleotide-nucleotide comparisons for query sequences shorter than 50 nucleotides.
\item \code{task = "dc-megablast"} : Discontiguous megablast used to find somewhat distant sequences.
\item \code{task = "megablast"} : Traditional megablast used to find very similar (e.g., intraspecies or closely related species) sequences.
\item \code{task = "rmblastn"}
}}

\item{eval}{a character string specifying the e-value for BLAST based orthology inference. Please use the scientific notation.}

\item{ortho_detection}{a character string specifying the Orthology Inference method that shall be used to perform
dNdS computations. Possible options are: 
\itemize{
 \item \code{ortho_detection = "BH"}: BLAST best unidirectional hit
 \item \code{ortho_detection = "RBH"}: BLAST best reciprocal hit
}}

\item{max.target.seqs}{a numeric value specifying the number of aligned sequences to keep.
Please be aware that \code{max.target.seqs} selects best hits based on the database entry and not by the best e-value. See details here: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/bty833/5106166 .}

\item{min_qry_coverage_hsp}{minimum \code{qcovhsp} (= query coverage of the HSP) of an orthologous hit (a value between 1 and 100).}

\item{min_qry_perc_identity}{minimum \code{perc_identity} (= percent sequence identity between query and selected HSP) of an orthologous hit (a value between 1 and 100).}

\item{logical_connective}{character representing logical connective (either "AND" or "OR") if \code{min_alig_length} is not \code{NULL} filtering is done on \code{min_alig_length} and/or \code{min_qry_perc_identity}}

\item{min_alig_length}{minimum \code{alig_length} (alignment length) to an orthologous hit (number of aligned nucleotides or amino acids depending on the input data)}

\item{comp_cores}{number of computing cores that shall be used to perform parallelized computations.}

\item{progress_bar}{should a progress bar be shown. Default is \code{progress_bar = TRUE}.}

\item{sep}{a file separator that is used to store maps as csv file.}

\item{path}{a character string specifying the path to the corresponding orthology inference tool.
For "BH" and "RBH": path to BLAST, "PO": path to ProteinOrtho 5.07, "OrthoMCL": path to OrthoMCL.}

\item{...}{additional parameters that shall be passed to  \code{\link{dNdS}}.}
}
\description{
Inference of orthologous lncRNAs between multiple species is performed via pairwise BLAST (reciprocal) best hit comparisons.
 The corresponding orthologous tables are then stored in an output folder.
}
\details{
Given a query organism and a set of subject organsisms that are stored in the same folder,
this function crawls through all subject organsism and infers the lncRNA homologs in
pairwise species comparisons.
}
\note{
According to Sarropoulos, I., et al. (2019) orthology detection of lncRNAs was performed by reciprocal BLAST searches. Significant hits with an e-value <= 10-3 were selected having an alignment identity >= 10\% OR a minimum alignment length >= 50 nucleotides.
}
\examples{
\dontrun{
# example using classic blastn searches
map_generator_lnc(
   query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
   subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
   output_folder   = "orthologs_lncrna",
   comp_cores      = 1
)
# example using  discontiguous megablast used to find somewhat distant sequences
map_generator_lnc(
   query_file      = system.file('seqs/ortho_thal_cds.fasta', package = 'orthologr'),
   subjects_folder = system.file('seqs/map_gen_example', package = 'orthologr'),
   output_folder   = "orthologs_lncrna",
   task            = "dc-megablast",
   comp_cores      = 1
)
}

\dontrun{
# parameter settings based on Sarropoulos, I., et al. (2019)
map_generator_lnc(
   query_file,,
   subjects_folder,
   eval                  = 1E-3,
   ortho_detection       = "RBH",
   output_folder,
   min_qry_coverage_hsp  = 0,
   min_qry_perc_identity = 10,
   logical_connective    = "OR",
   min_alig_length       = 50)
}
}
\references{
{
\insertRef{Sarropoulos2019}{orthologr}
}
}
\author{
Hajk-Georg Drost
}
