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\name{makeTxDbFromGFF}
\alias{makeTxDbFromGFF}
\title{
Make a TxDb object from annotations available as a
GFF3 or GTF file
}
\description{
The \code{makeTxDbFromGFF} function allows the user to make a
\link[GenomicFeatures]{TxDb} object from transcript annotations
available as a GFF3 or GTF file.
}
\usage{
makeTxDbFromGFF(file,
format=c("auto", "gff3", "gtf"),
dataSource=NA,
organism=NA,
taxonomyId=NA,
circ_seqs=NULL,
chrominfo=NULL,
miRBaseBuild=NA,
metadata=NULL,
dbxrefTag)
}
\arguments{
\item{file}{
Input GFF3 or GTF file. Can be a path to a file, or an URL,
or a connection object, or a \link[rtracklayer]{GFF3File}
or \link[rtracklayer]{GTFFile} object.
}
\item{format}{
Format of the input file. Accepted values are: \code{"auto"} (the
default) for auto-detection of the format, \code{"gff3"}, or \code{"gtf"}.
Use \code{"gff3"} or \code{"gtf"} only if auto-detection failed.
}
\item{dataSource}{
A single string describing the origin of the data file. Please be as
specific as possible.
}
\item{organism}{
What is the Genus and species of this organism. Please use proper
scientific nomenclature for example: "Homo sapiens" or "Canis familiaris"
and not "human" or "my fuzzy buddy". If properly written, this information
may be used by the software to help you out later.
}
\item{taxonomyId}{
By default this value is NA and the organism provided will be used to
look up the correct value for this. But you can use this argument to
override that and supply your own taxonomy id here (which will be
separately validated). Since providing a valid taxonomy id will not
require us to look up one based on your organism: this is one way that
you can loosen the restrictions about what is and isn't a valid value
for the organism.
}
\item{circ_seqs}{
A character vector to list out which chromosomes should be marked as
circular.
}
\item{chrominfo}{
Data frame containing information about the chromosomes. Will be
passed to the internal call to \code{\link{makeTxDb}}.
See \code{?\link{makeTxDb}} for more information.
Alternatively, can be a \link[GenomeInfoDb]{Seqinfo} object.
}
\item{miRBaseBuild}{
Specify the string for the appropriate build Information from mirbase.db
to use for microRNAs. This can be learned by calling
\code{supportedMiRBaseBuildValues}. By default, this value will be set to
\code{NA}, which will inactivate the \code{microRNAs} accessor.
}
\item{metadata}{
A 2-column data frame containing meta information to be included in the
\link[GenomicFeatures]{TxDb} object. See \code{?\link{makeTxDb}} for more
information about the format of \code{metadata}.
}
\item{dbxrefTag}{
If not missing, the values in the \code{Dbxref} attribute with the
specified tag (like \dQuote{GeneID}) are used for the feature names.
}
}
\details{
\code{makeTxDbFromGFF} is a convenience function that feeds
data from the parsed file to the \code{\link{makeTxDbFromGRanges}}
function.
}
\value{A \link[GenomicFeatures]{TxDb} object.}
\author{
H. Pagès and M. Carlson
}
\seealso{
\itemize{
\item \code{\link{makeTxDbFromGRanges}}, which \code{makeTxDbFromGFF}
is based on, for making a \link[GenomicFeatures]{TxDb} object
from a \link[GenomicRanges]{GRanges} object.
\item The \code{\link[BiocIO]{import}} function in the
\pkg{rtracklayer} package (also used by \code{makeTxDbFromGFF}
internally).
\item \code{\link{makeTxDbFromUCSC}}, \code{\link{makeTxDbFromBiomart}},
and \code{\link{makeTxDbFromEnsembl}}, for making a
\link[GenomicFeatures]{TxDb} object from online resources.
\item The \code{\link{supportedMiRBaseBuildValues}} function for
listing all the possible values for the \code{miRBaseBuild}
argument.
\item \link[GenomicFeatures]{TxDb} objects implemented in the
\pkg{GenomicFeatures} package.
\item \code{\link{makeTxDb}} for the low-level function used
by the \code{makeTxDbFrom*} functions to make the
\link[GenomicFeatures]{TxDb} object returned to the user.
}
}
\examples{
## TESTING GFF3
gffFile <- system.file("extdata", "GFF3_files", "a.gff3", package="txdbmaker")
txdb <- makeTxDbFromGFF(gffFile,
dataSource="partial gtf file for Tomatoes for testing",
organism="Solanum lycopersicum")
## TESTING GTF, this time specifying some metadata and the chrominfo
gtfFile <- system.file("extdata", "GTF_files",
"GCA_002204515.1_AaegL5.0_genomic.gtf.gz",
package="txdbmaker")
resource_url <- paste0("ftp.ncbi.nlm.nih.gov/genomes/all/GCA/002/204/515/",
"GCA_002204515.1_AaegL5.0/")
metadata <- data.frame(name="Resource URL", value=resource_url)
chrominfo <- data.frame(chrom="MF194022.1",
length=16790,
is_circular=TRUE,
genome="AaegL5.0")
txdb2 <- makeTxDbFromGFF(gtfFile,
dataSource="NCBI",
organism="Aedes aegypti",
chrominfo=chrominfo,
metadata=metadata)
}
|
