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\name{makeTxDb}
\alias{makeTxDb}
\title{
Making a TxDb object from user supplied annotations
}
\description{
\code{makeTxDb} is a low-level constructor for making
a \link{TxDb} object from user supplied transcript annotations.
Note that the end user will rarely need to use \code{makeTxDb} directly
but will typically use one of the high-level constructors
\code{\link{makeTxDbFromUCSC}}, \code{\link{makeTxDbFromEnsembl}},
or \code{\link{makeTxDbFromGFF}}.
}
\usage{
makeTxDb(transcripts, splicings, genes=NULL,
chrominfo=NULL, metadata=NULL,
reassign.ids=FALSE, on.foreign.transcripts=c("error", "drop"))
}
\arguments{
\item{transcripts}{
Data frame containing the genomic locations of a set of transcripts.
}
\item{splicings}{
Data frame containing the exon and CDS locations of a set of transcripts.
}
\item{genes}{
Data frame containing the genes associated to a set of transcripts.
}
\item{chrominfo}{
Data frame containing information about the chromosomes hosting
the set of transcripts.
}
\item{metadata}{
2-column data frame containing meta information about this set of
transcripts like organism, genome, UCSC table, etc...
The names of the columns must be \code{"name"} and \code{"value"}
and their type must be character.
}
\item{reassign.ids}{
\code{TRUE} or \code{FALSE}.
Controls how internal ids should be assigned for each type of feature
i.e. for transcripts, exons, and CDS. For each type, if \code{reassign.ids}
is \code{FALSE} (the default) and if the ids are supplied, then they
are used as the internal ids, otherwise the internal ids are assigned
in a way that is compatible with the order defined by ordering the
features first by chromosome, then by strand, then by start, and
finally by end.
}
\item{on.foreign.transcripts}{
Controls what to do when the input contains \emph{foreign transcripts}
i.e. transcripts that are on sequences not in \code{chrominfo}.
If set to \code{"error"} (the default)
}
}
\details{
The \code{transcripts} (required), \code{splicings} (required)
and \code{genes} (optional) arguments must be data frames that
describe a set of transcripts and the genomic features related
to them (exons, CDS and genes at the moment).
The \code{chrominfo} (optional) argument must be a data frame
containing chromosome information like the length of each chromosome.
\code{transcripts} must have 1 row per transcript and the following
columns:
\itemize{
\item \code{tx_id}: Transcript ID. Integer vector. No NAs. No duplicates.
\item \code{tx_chrom}: Transcript chromosome. Character vector (or factor)
with no NAs.
\item \code{tx_strand}: Transcript strand. Character vector (or factor)
with no NAs where each element is either \code{"+"} or \code{"-"}.
\item \code{tx_start}, \code{tx_end}: Transcript start and end.
Integer vectors with no NAs.
\item \code{tx_name}: [optional] Transcript name. Character vector (or
factor). NAs and/or duplicates are ok.
\item \code{tx_type}: [optional] Transcript type (e.g. mRNA, ncRNA, snoRNA,
etc...). Character vector (or factor). NAs and/or duplicates are ok.
\item \code{gene_id}: [optional] Associated gene. Character vector (or
factor). NAs and/or duplicates are ok.
}
Other columns, if any, are ignored (with a warning).
\code{splicings} must have N rows per transcript, where N is the nb
of exons in the transcript. Each row describes an exon plus, optionally,
the CDS contained in this exon. Its columns must be:
\itemize{
\item \code{tx_id}: Foreign key that links each row in the \code{splicings}
data frame to a unique row in the \code{transcripts} data frame.
Note that more than 1 row in \code{splicings} can be linked to the
same row in \code{transcripts} (many-to-one relationship).
Same type as \code{transcripts$tx_id} (integer vector). No NAs.
All the values in this column must be present in
\code{transcripts$tx_id}.
\item \code{exon_rank}: The rank of the exon in the transcript.
Integer vector with no NAs. (\code{tx_id}, \code{exon_rank})
pairs must be unique.
\item \code{exon_id}: [optional] Exon ID.
Integer vector with no NAs.
\item \code{exon_name}: [optional] Exon name. Character vector (or factor).
NAs and/or duplicates are ok.
\item \code{exon_chrom}: [optional] Exon chromosome.
Character vector (or factor) with no NAs.
If missing then \code{transcripts$tx_chrom} is used.
If present then \code{exon_strand} must also be present.
\item \code{exon_strand}: [optional] Exon strand.
Character vector (or factor) with no NAs.
If missing then \code{transcripts$tx_strand} is used
and \code{exon_chrom} must also be missing.
\item \code{exon_start}, \code{exon_end}: Exon start and end.
Integer vectors with no NAs.
\item \code{cds_id}: [optional] CDS ID. Integer vector.
If present then \code{cds_start} and \code{cds_end} must also
be present.
NAs are allowed and must match those in \code{cds_start} and
\code{cds_end}.
\item \code{cds_name}: [optional] CDS name. Character vector (or factor).
If present then \code{cds_start} and \code{cds_end} must also be
present. NAs and/or duplicates are ok. Must contain NAs at least
where \code{cds_start} and \code{cds_end} contain them.
\item \code{cds_start}, \code{cds_end}: [optional] CDS start and end.
Integer vectors.
If one of the 2 columns is missing then all \code{cds_*} columns
must be missing.
NAs are allowed and must occur at the same positions in
\code{cds_start} and \code{cds_end}.
\item \code{cds_phase}: [optional] CDS phase. Integer vector.
If present then \code{cds_start} and \code{cds_end} must also
be present.
NAs are allowed and must match those in \code{cds_start} and
\code{cds_end}.
}
Other columns, if any, are ignored (with a warning).
\code{genes} should not be supplied if \code{transcripts} has a
\code{gene_id} column. If supplied, it must have N rows per transcript,
where N is the nb of genes linked to the transcript (N will be 1 most
of the time). Its columns must be:
\itemize{
\item \code{tx_id}: [optional] \code{genes} must have either a
\code{tx_id} or a \code{tx_name} column but not both.
Like \code{splicings$tx_id}, this is a foreign key that
links each row in the \code{genes} data frame to a unique
row in the \code{transcripts} data frame.
\item \code{tx_name}: [optional]
Can be used as an alternative to the \code{genes$tx_id}
foreign key.
\item \code{gene_id}: Gene ID. Character vector (or factor). No NAs.
}
Other columns, if any, are ignored (with a warning).
\code{chrominfo} must have 1 row per chromosome and the following
columns:
\itemize{
\item \code{chrom}: Chromosome name.
Character vector (or factor) with no NAs and no duplicates.
\item \code{length}: Chromosome length.
Integer vector with either all NAs or no NAs.
\item \code{is_circular}: [optional] Chromosome circularity flag.
Logical vector. NAs are ok.
}
Other columns, if any, are ignored (with a warning).
}
\value{A \link{TxDb} object.}
\author{Hervé Pagès}
\seealso{
\itemize{
\item \code{\link{makeTxDbFromUCSC}}, \code{\link{makeTxDbFromBiomart}},
and \code{\link{makeTxDbFromEnsembl}}, for making a \link{TxDb}
object from online resources.
\item \code{\link{makeTxDbFromGRanges}} and \code{\link{makeTxDbFromGFF}}
for making a \link{TxDb} object from a \link[GenomicRanges]{GRanges}
object, or from a GFF or GTF file.
\item The \link{TxDb} class.
\item \code{\link[AnnotationDbi]{saveDb}} and
\code{\link[AnnotationDbi]{loadDb}} in the \pkg{AnnotationDbi}
package for saving and loading a \link{TxDb} object as an SQLite
file.
}
}
\examples{
transcripts <- data.frame(
tx_id=1:3,
tx_chrom="chr1",
tx_strand=c("-", "+", "+"),
tx_start=c(1, 2001, 2001),
tx_end=c(999, 2199, 2199))
splicings <- data.frame(
tx_id=c(1L, 2L, 2L, 2L, 3L, 3L),
exon_rank=c(1, 1, 2, 3, 1, 2),
exon_start=c(1, 2001, 2101, 2131, 2001, 2131),
exon_end=c(999, 2085, 2144, 2199, 2085, 2199),
cds_start=c(1, 2022, 2101, 2131, NA, NA),
cds_end=c(999, 2085, 2144, 2193, NA, NA),
cds_phase=c(0, 0, 2, 0, NA, NA))
txdb <- makeTxDb(transcripts, splicings)
}
|
