run_tximport: Run tximport

In BgeeDB/BgeeCall: Automatic RNA-Seq present/absent gene expression calls generation

Run tximport

Description

Run tximport. Will summarize abundance estimation from transcript level to gene level if 'myAbundanceMetadata@txout == FALSE'. Otherwise keep abundance estimation at transcript level.

Usage

run_tximport(
  myAbundanceMetadata = new("KallistoMetadata"),
  myBgeeMetadata = new("BgeeMetadata"),
  myUserMetadata,
  abundanceFile = ""
)

Arguments

myAbundanceMetadata	A descendant object of the Class myAbundanceMetadata.
myBgeeMetadata	A Reference Class BgeeMetadata object.
myUserMetadata	A Reference Class UserMetadata object.
abundanceFile	(Optional) Path to the abundance file. NULL by default. If not NULL, the file located at 'abundanceFile' will be used to run tximport. Otherwise (Default) the path to the abundance file is deduced fom attributes of classes 'BgeeMetadata', 'UserMetadata' and 'AbundanceMetadata'

Value

a tximport object

Author(s)

Julien Wollbrett

Examples

{
user <- new("UserMetadata", working_path = system.file("extdata", 
    package = "BgeeCall"), species_id = "6239", 
  rnaseq_lib_path = system.file("extdata", 
    "SRX099901_subset", package = "BgeeCall"), 
  annotation_name = "WBcel235_84", simple_arborescence = TRUE)
abundance_file <- system.file('extdata', 'abundance.tsv', package = 'BgeeCall')
tx_import <- run_tximport(myUserMetadata = user, 
abundanceFile = abundance_file)
}

BgeeDB/BgeeCall documentation built on Nov. 10, 2023, 5:40 a.m.