tr2g_gff3: Get transcript and gene info from GFF3 file
In sarangian/deaRscripts: 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

This function reads a GFF3 file and extracts the transcript ID and corresponding gene ID. This function assumes that the GFF3 file is properly formatted. See http://gmod.org/wiki/GFF3 for a detailed description of proper GFF3 format. Note that GTF files have a somewhat different and simpler format in the attribute field, which this function does not support. See http://mblab.wustl.edu/GTF2.html for a detailed description of proper GTF format. To extract transcript and gene information from GTF files, see the function tr2g_gtf in this package. Some files bearing the .gff3 are in fact more like the GTF format. If this is so, then change the extension to .gtf and use the function tr2g_gtf in this package instead.

tr2g_gff3(file, type_use = "mRNA", transcript_id = "transcript_id",
  gene_id = "gene_id", gene_name = "Name",
  transcript_version = "version", gene_version = "version",
  version_sep = ".", verbose = TRUE)

`file`	Path to a GTF file to be read. The file can remain gzipped.
`type_use`	Character vector, the values taken by the `type` field in the GTF file that denote the desired transcripts. This can be "exon", "transcript", "mRNA", and etc.
`transcript_id`	Character vector of length 1. Tag in `attribute` field corresponding to transcript IDs. This argument must be supplied and cannot be `NA` or `NULL`. Will throw error if tag indicated in this argument does not exist.
`gene_id`	Character vector of length 1. Tag in `attribute` field corresponding to gene IDs. This argument must be supplied and cannot be `NA` or `NULL`. Note that this is different from gene symbols, which do not have to be unique. This can be Ensembl or Entrez IDs. However, if the gene symbols are in fact unique for each gene, you may supply the tag for human readable gene symbols to this argument. Will throw error if tag indicated in this argument does not exist.
`gene_name`	Character vector of length 1. Tag in `attribute` field corresponding to gene symbols. This argument can be `NA` or `NULL` if you are fine with non-human readable gene IDs and do not wish to extract human readable gene symbols.
`transcript_version`	Character vector of length 1. Tag in `attribute` field corresponding to transcript version number. If your GTF file does not include transcript version numbers, or if you do not wish to include the version number, then use `NULL` for this argument. 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.
`gene_version`	Character vector of length 1. Tag in `attribute` field corresponding to gene version number. If your GTF file does not include gene version numbers, or if you do not wish to include the version number, then use `NULL` for this argument. Unlike transcript version number, it's up to you whether to include gene version number.
`version_sep`	Character to separate bewteen the main ID and the version number. Defaults to ".", as in Ensembl.
`verbose`	Whether to display progress.

Transcript and gene versions may not be present in all GTF files, so these arguments are optional. This function has arguments for transcript and gene version numbers because Ensembl IDs have version numbers. For Ensembl IDs, we recommend including the version number, since a change in version number signals a change in the entity referred to by the ID after reannotation. If a version is used, then it will be appended to the ID, separated by version_sep.

The transcript and gene IDs are The attribute field (the last field) of GTF files can be complicated and inconsistent across different sources. Please check the attribute tags in your GTF file and consider the arguments of this function carefully. The defaults are set according to Ensembl GTF files; defaults may not work for files from other sources. Due to the general lack of standards for the attribute field, you may need to further clean up the output of this function.

A data frame 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_fasta, tr2g_gtf, transcript2gene

toy_path <- system.file("testdata", package = "BUSpaRse")
file_use <- paste(toy_path, "gff3_test.gff3", sep = "/")
# Default
tr2g <- tr2g_gff3(file = file_use, verbose = FALSE)
# Excluding version numbers
tr2g <- tr2g_gff3(file = file_use, transcript_version = NULL,
  gene_version = NULL)