run_kallisto {BgeeCall} | R Documentation |
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
run_kallisto( myKallistoMetadata, myBgeeMetadata, myUserMetadata, transcriptome_path = "" )
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. |
create kallisto output files and save them on the hard drive
Julien Wollbrett.
## 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)