makeTxdbFromGenome: Make txdb from genome

In JokingHero/ORFik: Open Reading Frames in Genomics

Make txdb from genome

Description

Make a Txdb with defined seqlevels and seqlevelsstyle from the fasta genome. This makes it more fail safe than standard Txdb creation. Example is that you can not create a coverage window outside the chromosome boundary, this is only possible if you have set the seqlengths.

Usage

makeTxdbFromGenome(
  gtf,
  genome = NULL,
  organism,
  optimize = FALSE,
  gene_symbols = FALSE,
  uniprot_id = FALSE,
  pseudo_5UTRS_if_needed = NULL,
  minimum_5UTR_percentage = 30,
  return = is.null(txdb_file_out_path),
  txdb_file_out_path = paste0(gtf, ".db"),
  symbols_file_out_path = file.path(dirname(gtf), "gene_symbol_tx_table.fst")
)

Arguments

gtf	path to gtf file
genome	character, default NULL. Path to fasta genome corresponding to the gtf. If NULL, can not set seqlevels. If value is NULL or FALSE, it will be ignored.
organism	Scientific name of organism, first letter must be capital! Example: Homo sapiens. Will force first letter to capital and convert any "_" (underscore) to " " (space)
optimize	logical, default FALSE. Create a folder within the output folder (defined by txdb_file_out_path), that includes optimized objects to speed up loading of annotation regions from up to 15 seconds on human genome down to 0.1 second. ORFik will then load these optimized objects instead. Currently optimizes filterTranscript() function and loadRegion() function for 5' UTRs, 3' UTRs, CDS, mRNA (all transcript with CDS) and tx (all transcripts).
gene_symbols	logical default FALSE. If TRUE, will download and store all gene symbols for all transcripts (coding and noncoding)- In a file called: "gene_symbol_tx_table.fst" in same folder as txdb. hgcn for human, mouse symbols for mouse and rat, more to be added.
uniprot_id	logical default FALSE. If TRUE, will download and store all uniprot id for all transcripts (coding and noncoding)- In a file called: "gene_symbol_tx_table.fst" in same folder as txdb.
pseudo_5UTRS_if_needed	integer, default NULL. If defined > 0, will add pseudo 5' UTRs of maximum this length if 'minimum_5UTR_percentage" (default 30 mRNAs (coding transcripts) do not have a leader. (NULL and 0 are both the ignore command)
minimum_5UTR_percentage	numeric, default 30. What minimum percentage of mRNAs most have a 5' UTRs (leaders), to not do the pseudo_UTR addition. If percentage is higher, addition is ignored, set to 101 to always do it.
return	logical, default FALSE. If TRUE, return TXDB object, else invisible(NULL).
txdb_file_out_path	character path, default paste0(gtf, ".db"). Set to NULL to not write file to disc.
symbols_file_out_path	character path, default file.path(dirname(gtf), "gene_symbol_tx_table.fst"). Must be defined as character if "gene_symbols" is TRUE. Ignored if "gene_symbols" is FALSE.

Value

logical, default is.null(txdb_file_out_path), Txdb saved to disc named default paste0(gtf, ".db"). Set 'return' argument to TRUE, to also get txdb back as an object.

Examples

gtf <- "/path/to/local/annotation.gtf"
genome <- "/path/to/local/genome.fasta"
#makeTxdbFromGenome(gtf, genome, organism = "Saccharomyces cerevisiae")
# Runnable full example
df <- ORFik.template.experiment()
gtf <- sub("\\.db$", "", df@txdb)
genome <- df@fafile
txdb <- makeTxdbFromGenome(gtf, genome, organism = "Saccharomyces cerevisiae",
  txdb_file_out_path = NULL)
## Add pseudo UTRs if needed (< 30% of cds have a defined 5'UTR)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.