% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/generate_ortholog_tables.R
\name{generate_ortholog_tables}
\alias{generate_ortholog_tables}
\title{Generate ortholog tables by gene locus and splice varaint}
\usage{
generate_ortholog_tables(
  dNdS_file,
  annotation_file_query,
  annotation_file_subject,
  output_folder = getwd(),
  output_type = "gene_locus",
  format
)
}
\arguments{
\item{dNdS_file}{file path to a \code{dNdS_tbl} generated with \code{\link{dNdS}} and
stored conform with \code{\link{read.dnds.tbl}}.}

\item{annotation_file_query}{file path to the annotation file of the query species in \code{gtf} or \code{gff} file format.}

\item{annotation_file_subject}{file path to the annotation file of the subject species in \code{gtf} or \code{gff} file format.}

\item{output_folder}{file path to a folder in which orthologs tables shall be stored.}

\item{output_type}{type of ortholog table that shall be printed out (or stored in a variable).
Available options are:
\itemize{
\item \code{output_type = "gene_locus"} (Default): find for each gene locus a representative splice variant that
maximizes the sequence homology (in terms of smalles e-value and longest splice variant in case of same evalue) 
to the subject gene locus and its representative splice variant. The output table contains only once representative splice variant per gene locus.
\item \code{output_type = "splice_variant"}: for each homologous gene locus determine for each splice variant their
respective splice variant homolog. he output table contains several splice variants and their homologous splice variants per gene locus.
}}

\item{format}{a vector of length 2 storing the annotation file formats of the query annotation file and subject annotation file: either \code{gtf} or \code{gff} format. E.g. \code{format = c("gtf","gtf")}.}
}
\description{
Given an input dNdS table generated by \code{\link{dNdS}} and
annotation files for the query and subject species in \code{gtf} or \code{gff}
file format, this function selects the best BLAST hit to represent either a gene locus (e.g. the splice variant of the gene locus with lowest e-value) or the best BLAST hit for a splice varaint.
}
\author{
Hajk-Georg Drost
}
