create_kallisto_index: Create kallisto indexes.

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

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)

BgeeCall documentation built on Dec. 12, 2020, 2 a.m.