Make a Tx2Gene object from transcriptome FASTA

makeTx2GeneFromFASTA(file, source = c("ensembl", "gencode", "flybase",
  "wormbase"))

Arguments

file

character(1). File path.

source

character(1). FASTA file source:

  • "ensembl": Ensembl.

  • "gencode": GENCODE.

  • "flybase": FlyBase.

  • "wormbase": WormBase.

Assuming Ensembl transcriptome (i.e. cDNA) input by default.

Value

Tx2Gene.

Note

RefSeq transcript FASTA (e.g. "GRCh38_latest_rna.fna.gz") doesn't contain gene identifiers, and is not supported.

Updated 2019-11-06.

See also

tx2gene importers defined in koopa.

Examples

## Ensembl ==== file <- pasteURL( "ftp.ensembl.org", "pub", "release-98", "fasta", "homo_sapiens", "cdna", "Homo_sapiens.GRCh38.cdna.all.fa.gz", protocol = "ftp" ) ## > makeTx2GeneFromFASTA(file, source = "ensembl") ## GENCODE ==== file <- pasteURL( "ftp.ebi.ac.uk", "pub", "databases", "gencode", "Gencode_human", "release_32", "gencode.v32.transcripts.fa.gz", protocol = "ftp" ) ## > makeTx2GeneFromFASTA(file, source = "gencode") ## FlyBase ==== file <- pasteURL( "ftp.flybase.net", "releases", "FB2019_05", "dmel_r6.30", "fasta", "dmel-all-transcript-r6.30.fasta.gz", protocol = "ftp" ) ## > makeTx2GeneFromFASTA(file, source = "flybase") ## WormBase ==== file <- pasteURL( "ftp.wormbase.org", "pub", "wormbase", "releases", "WS272", "species", "c_elegans", "PRJNA13758", "c_elegans.PRJNA13758.WS272.mRNA_transcripts.fa.gz", protocol = "ftp" ) ## > makeTx2GeneFromFASTA(file, source = "wormbase")