run_tximport {BgeeCall} | R Documentation

## 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)
    }

[Package BgeeCall version 1.3.1 Index]