create_kallisto_index {BgeeCall} | R Documentation |
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.
create_kallisto_index( myKallistoMetadata, myBgeeMetadata, myUserMetadata, transcriptome_path = "" )
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 |
create kallisto index and save it 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. 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)