% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/ltr.cn.R
\name{ltr.cn}
\alias{ltr.cn}
\title{Copy Number Quantification of predicted LTRs (solo LTR prediction)}
\usage{
ltr.cn(
  data.sheet,
  LTR.fasta_3ltr,
  LTR.fasta_5ltr,
  genome,
  ltr.similarity = 70,
  scope.cutoff = 0.85,
  perc.ident.cutoff = 70,
  output = NULL,
  max.hits = 500,
  eval = 1e-10,
  cores = 1
)
}
\arguments{
\item{data.sheet}{path to the \code{*_LTRpred_DataSheet.csv} file generated by \code{\link{LTRpred}}.}

\item{LTR.fasta_3ltr}{path to fasta file storing sequences of 3 prime LTRs generated by \code{\link{LTRpred}}.}

\item{LTR.fasta_5ltr}{path to fasta file storing sequences of 5 prime LTRs generated by \code{\link{LTRpred}}.}

\item{genome}{file path to the reference genome in which solo LTRs shall be found (in \code{fasta} format).}

\item{ltr.similarity}{similarity threshold for defining LTR similarity.}

\item{scope.cutoff}{similarity threshold for the scope variable. The scope of a BLAST hit is defined by \code{abs(s_len - alig_length) / s_len}
and aims to quantify the scope ('length similarity between hit and query') of the alignment. Default is \code{scope.cutoff = 0.85} meaning that
at least 85\% of the length of the query sequence must match with the length of the subject sequence.}

\item{perc.ident.cutoff}{choose the minimum sequence identity between the query sequence and subject hit sequence that have a scope >= \code{scope.cutoff} (e.g. 0.85). 
Default is \code{perc.ident.cutoff = 70}. This threshold aims to detect BLAST hits that have similar sequence lengths 
(controlled by the \code{scope.cutoff} variable; e.g. \code{scope.cutoff = 0.85}) and within this scope at least e.g. 70\% sequence identity (controlled by the \code{perc.ident.cutoff} variable).}

\item{output}{file name of the BLAST output. If \code{output = NULL} (default) then the BLAST output file will be deleted after the result \code{data.frame} is returned by this function.}

\item{max.hits}{maximum number of hits that shall be retrieved that still fulfill the e-value criterium.
Default is \code{max.hits = 65000}.}

\item{eval}{e-value threshold for BLAST hit detection. Default is \code{eval = 1E-10}.}

\item{cores}{number of cores for parallel computations.}
}
\description{
Detect solo LTR copies and genomic locations of predicted LTR transposons using a BLAST search strategy.
}
\references{
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990) "Basic local alignment search tool." J. Mol. Biol. 215:403-410.

Gish, W. & States, D.J. (1993) "Identification of protein coding regions by database similarity search." Nature Genet. 3:266-272.

Madden, T.L., Tatusov, R.L. & Zhang, J. (1996) "Applications of network BLAST server" Meth. Enzymol. 266:131-141.

Altschul, S.F., Madden, T.L., Schaeffer, A.A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D.J. (1997) "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs." Nucleic Acids Res. 25:3389-3402.

Zhang Z., Schwartz S., Wagner L., & Miller W. (2000), "A greedy algorithm for aligning DNA sequences" J Comput Biol 2000; 7(1-2):203-14.
}
\author{
Hajk-Georg Drost
}
