create_kallisto_index {BgeeCall} | R Documentation

## Create kallisto indexes.

### Description

This function creates kallisto indexes. Two indexes can be created depending on the reads size (see 'AbundanceMetadata@read_size_kmer_threshold' and 'UserMetadata@reads_size' for more information). One with default kmer value (31 nt) and one with kmer size of 15 nt. In order to generate.

### Usage

    create_kallisto_index(
      myKallistoMetadata,
      myBgeeMetadata,
      myUserMetadata,
      transcriptome_path = ""
    )

### Arguments

`myKallistoMetadata` | A Reference Class KallistoMetadata object.
`myBgeeMetadata` | A Reference Class BgeeMetadata object.
`myUserMetadata` | A Reference Class UserMetadata object.
`transcriptome_path` | path to the transcriptome fasta file. If no path is provided the default path created using BgeeCall will be used. IMPORTANT : in BgeeCall the transcriptome used to generate present/absent calls contains both intergenic sequences downloaded from Bgee and the reference transcriptome. If this function is run to generate present/absent then 'transcriptome_path' has to be empty

### Value

create kallisto index and save it on the hard drive

### Author(s)

Julien Wollbrett.

### Examples

    ## Not run:
    # first a transcriptome is needed. Here it is downloaded from AnnotationHub
    library(AnnotationHub)
    ah <- AnnotationHub()
    ah_resources <- query(ah, c('Ensembl', 'Caenorhabditis elegans', '84'))

    # kallisto can not deal with S4 objects. A Path to a transcriptome file is
    # required
    transcriptome_object <- rtracklayer::import.2bit(ah_resources[['AH50453']])
    transcriptome_path <- file.path(getwd(),'transcriptome.fa')
    Biostrings::writeXStringSet(transcriptome_object, transcriptome_path)

    # initialize objects needed to create destination folder
    bgee <- new('BgeeMetadata')
    user <- new('UserMetadata', species_id = '6239')
    kallisto <- new('KallistoMetadata')

    # generate transcriptome index
    create_kallisto_index(kallisto, bgee, user, transcriptome_path)

    ## End(Not run)

[Package BgeeCall version 1.8.0 Index]