Wrapper for GenomicFeatures makeTxDbFromGFF importer.

makeTxDbFromGFF(file)

Arguments

file

character(1). File path.

Value

TxDb.

Functions

  • makeTxDbFromGFF: Primary function.

Note

Updated 2021-02-26.

See also

Examples

## 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) ## > seqinfo(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) ## > seqinfo(txdb)