makeTxDbFromGFF: Make TxDb from a GFF/GTF file

Description Usage Arguments Value Functions Note See Also Examples

View source: R/makeTxDbFromGFF.R

Description

Wrapper for GenomicFeatures makeTxDbFromGFF importer.

Usage

1

Arguments

file

character(1). File path.

Value

TxDb.

Functions

Note

Updated 2021-08-09.

See Also

Examples

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## GENCODE ====
## > gtfFile <- pasteURL(
## >     "ftp.ebi.ac.uk",
## >     "pub",
## >     "databases",
## >     "gencode",
## >     "Gencode_human",
## >     "release_36",
## >     "gencode.v36.annotation.gtf.gz",
## >     protocol = "ftp"
## > )
## > txdb <- AcidGenomes::makeTxDbFromGFF(file = gtfFile)
## > print(txdb)

## RefSeq ====
## > gffFile <- pasteURL(
## >     "ftp.ncbi.nlm.nih.gov",
## >     "genomes",
## >     "refseq",
## >     "vertebrate_mammalian",
## >     "Homo_sapiens",
## >     "all_assembly_versions",
## >     "GCF_000001405.38_GRCh38.p12",
## >     "GCF_000001405.38_GRCh38.p12_genomic.gff.gz",
## >     protocol = "ftp"
## > )
## > txdb <- AcidGenomes::makeTxDbFromGFF(file = gffFile)
## > print(txdb)

acidgenomics/AcidGenomes documentation built on Sept. 16, 2021, 7:30 p.m.