run_kallisto: Run one kallisto abundance analyse

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

Description

Run kallisto and all preliminary steps if needed like : - creation of transcriptome with intergenic (if needed) - installation of kallisto (if needed) - index creation (if needed) - run kallisto quantification

Usage

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

Arguments

myKallistoMetadata	A Reference Class KallistoMetadata object.
myBgeeMetadata	A Reference Class BgeeMetadata object.
myUserMetadata	A Reference Class UserMetadata object. This object has to be edited before running kallisto @seealso UserMetadata.R
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.

Value

create kallisto output files and save them 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. Path to 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')
user <- setRNASeqLibPath(user, system.file( 
                     'extdata', 'SRX099901_subset', 
                     package = 'BgeeCall'))
kallisto <- new('KallistoMetadata')

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

## End(Not run)

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