makeTx2GeneFromFASTA: Make a Tx2Gene object from transcriptome FASTA

Description Usage Arguments Value Note Examples

View source: R/makeTx2GeneFromFASTA.R

Description

Make a Tx2Gene object from transcriptome FASTA

Usage

1

Arguments

file

character(1). File path.

Value

Tx2Gene.

Note

RefSeq transcript FASTA (e.g. "GCF_000001405.39_GRCh38.p13_rna.fna.gz") doesn't contain gene identifiers, and is not supported.

Updated 2021-01-29.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
## Ensembl ====
file <- pasteURL(
    "ftp.ensembl.org",
    "pub",
    "release-102",
    "fasta",
    "homo_sapiens",
    "cdna",
    "Homo_sapiens.GRCh38.cdna.all.fa.gz",
    protocol = "ftp"
)
t2g <- makeTx2GeneFromFASTA(file)
print(t2g)

## GENCODE ====
## > file <- pasteURL(
## >     "ftp.ebi.ac.uk",
## >     "pub",
## >     "databases",
## >     "gencode",
## >     "Gencode_human",
## >     "release_32",
## >     "gencode.v32.transcripts.fa.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTx2GeneFromFASTA(file)
## > print(t2g)

## FlyBase ====
## > file <- pasteURL(
## >     "ftp.flybase.net",
## >     "releases",
## >     "FB2019_05",
## >     "dmel_r6.30",
## >     "fasta",
## >     "dmel-all-transcript-r6.30.fasta.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTx2GeneFromFASTA(file)
## > print(t2g)

## WormBase ====
## > file <- pasteURL(
## >     "ftp.wormbase.org",
## >     "pub",
## >     "wormbase",
## >     "releases",
## >     "WS272",
## >     "species",
## >     "c_elegans",
## >     "PRJNA13758",
## >     "c_elegans.PRJNA13758.WS272.mRNA_transcripts.fa.gz",
## >     protocol = "ftp"
## > )
## > t2g <- makeTx2GeneFromFASTA(file)
## > print(t2g)

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