tr2g_fasta: Get transcript and gene info from names in FASTA files
In sarangian/RNASeqDEA: Differential Expression Analysis based on the read count data generated by either of Salmon, Kallisto, featureCounts and perform statistical analysis to discover quantitative changes in expression levels between two different experimental groups

Description Usage Arguments Details Value See Also Examples

FASTA files, such as those for cDNA and ncRNA from Ensembl, might have genome annotation information in the name of each sequence entry. This function extracts the transcript and gene IDs from such FASTA files.

1 2	tr2g_fasta(file, use_gene_name = TRUE, use_transcript_version = TRUE, use_gene_version = TRUE, verbose = TRUE)

`file`	Path to the FASTA file to be read. The file can remain gzipped.
`use_gene_name`	Logical, whether to get gene names.
`use_transcript_version`	Logical, whether to include version number in the Ensembl transcript ID. To decide whether to include transcript version number, check whether version numbers are included in the `transcripts.txt` in the `kallisto` output directory. If that file includes version numbers, then trannscript version numbers must be included here as well. If that file does not include version numbers, then transcript version numbers must not be included here.
`use_gene_version`	Logical, whether to include version number in the Ensembl gene ID. Unlike transcript version number, it's up to you whether to include gene version number.
`verbose`	Whether to display progress.

At present, this function only works with FASTA files from Ensembl, and uses regex to extract vertebrate Ensembl IDs. Sequence names should be formatted as follows:

ENST00000632684.1 cdna chromosome:GRCh38:7:142786213:142786224:1
gene:ENSG00000282431.1 gene_biotype:TR_D_gene transcript_biotype:TR_D_gene
gene_symbol:TRBD1 description:T cell receptor beta diversity 1
[Source:HGNC Symbol;Acc:HGNC:12158]

If your FASTA file sequence names are formatted differently, then you must extract the transcript and gene IDs by some other means. The Bioconductor package Biostrings is recommended; after reading the FASTA file into R, the sequence names can be accessed by the names function.

While normally, you should call sort_tr2g to sort the transcript IDs from the output of the tr2g_* family of functions, If the FASTA file supplied here is the same as the one used to build the kallisto index, then the transcript IDs in the output of this function are in the same order as in the kallisto index, so you can skip sort_tr2g and proceed directly to EC2gene with the output of this function.

A data frame with at least 2 columns: gene for gene ID, transcript for transcript ID, and optionally gene_name for gene names.

Other functions to retrieve transcript and gene info: sort_tr2g, tr2g_EnsDb, tr2g_TxDb, tr2g_ensembl, tr2g_gff3, tr2g_gtf, transcript2gene

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toy_path <- system.file("testdata", package = "BUSpaRse")
file_use <- paste(toy_path, "fasta_test.fasta", sep = "/")
tr2g <- tr2g_fasta(file = file_use, verbose = FALSE)