| makeTxDbFromGFF {GenomicFeatures} | R Documentation |
The makeTxDbFromGFF function allows the user
to make a TxDb object from transcript annotations
available as a GFF3 or GTF file.
makeTxDbFromGFF(file,
format=c("gff3","gtf"),
exonRankAttributeName=NA,
gffGeneIdAttributeName=NA,
chrominfo=NA,
dataSource=NA,
organism=NA,
circ_seqs=DEFAULT_CIRC_SEQS,
miRBaseBuild=NA,
useGenesAsTranscripts=FALSE,
gffTxName="mRNA",
species=NA)
file |
path/file to be processed |
format |
"gff3" or "gtf" depending on which file format you have to process |
exonRankAttributeName |
ignored and deprecated |
gffGeneIdAttributeName |
ignored and deprecated |
chrominfo |
data frame containing information about the
chromosomes. Will be passed to the internal call to
|
dataSource |
Where did this data file originate? Please be as specific as possible. |
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. |
circ_seqs |
a character vector to list out which chromosomes should be marked as circular. |
miRBaseBuild |
specify the string for the appropriate build
Information from mirbase.db to use for microRNAs. This can be
learned by calling |
useGenesAsTranscripts |
ignored and deprecated |
gffTxName |
ignored and deprecated |
species |
deprecated in favor of |
makeTxDbFromGFF is a convenience function that feeds
data from the parsed file to the makeTxDbFromGRanges
function.
A TxDb object.
M. Carlson and H. Pages
makeTxDbFromGRanges, which makeTxDbFromGFF
is based on, for making a TxDb object from a
GRanges object.
The import function in the
rtracklayer package (also used by makeTxDbFromGFF
internally).
makeTxDbFromUCSC and makeTxDbFromBiomart
for convenient ways to make a TxDb object from UCSC or BioMart
online resources.
The supportedMiRBaseBuildValues function for
listing all the possible values for the miRBaseBuild
argument.
The TxDb class.
makeTxDb for the low-level function used by the
makeTxDbFrom* functions to make the TxDb object
returned to the user.
## TESTING GFF3
gffFile <- system.file("extdata","GFF3_files","a.gff3",package="GenomicFeatures")
txdb <- makeTxDbFromGFF(file=gffFile,
format="gff3",
dataSource="partial gtf file for Tomatoes for testing",
organism="Solanum lycopersicum")
## TESTING GTF, this time specifying the chrominfo
gtfFile <- system.file("extdata","GTF_files","Aedes_aegypti.partial.gtf",
package="GenomicFeatures")
chrominfo <- data.frame(chrom = c('supercont1.1','supercont1.2'),
length=c(5220442, 5300000),
is_circular=c(FALSE, FALSE))
txdb2 <- makeTxDbFromGFF(file=gtfFile,
format="gtf",
chrominfo=chrominfo,
dataSource=paste("ftp://ftp.ensemblgenomes.org/pub/metazoa/",
"release-13/gtf/aedes_aegypti/",sep=""),
organism="Aedes aegypti")