Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/makeTxDbFromGFF.R
The makeTxDbFromGFF
function allows the user
to make a TxDb object from transcript annotations
available as a GFF3 or GTF file.
1 2 3 4 5 6 7 8 9 10 |
file |
Input GFF3 or GTF file. Can be a path to a file, or an URL, or a connection object, or a GFF3File or GTFFile object. |
format |
Format of the input file. Accepted values are: |
dataSource |
A single string describing the origin of the data file. 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. |
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. |
circ_seqs |
A character vector to list out which chromosomes should be marked as circular. |
chrominfo |
Data frame containing information about the chromosomes. Will be
passed to the internal call to |
miRBaseBuild |
Specify the string for the appropriate build Information from mirbase.db
to use for microRNAs. This can be learned by calling
|
metadata |
A 2-column data frame containing meta information to be included in the
TxDb object. See |
dbxrefTag |
If not missing, the values in the |
makeTxDbFromGFF
is a convenience function that feeds
data from the parsed file to the makeTxDbFromGRanges
function.
A TxDb object.
M. Carlson and H. Pagès
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
, makeTxDbFromBiomart
,
and makeTxDbFromEnsembl
, for making a TxDb
object from 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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## TESTING GFF3
gffFile <- system.file("extdata","GFF3_files","a.gff3",package="GenomicFeatures")
txdb <- makeTxDbFromGFF(file=gffFile,
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))
metadata <- data.frame(name="Resource URL",
value=paste0("ftp://ftp.ensemblgenomes.org/pub/metazoa/",
"release-13/gtf/aedes_aegypti/"))
txdb2 <- makeTxDbFromGFF(file=gtfFile,
chrominfo=chrominfo,
dataSource="ensemblgenomes",
organism="Aedes aegypti",
metadata=metadata)
|
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