linkedTxome {tximeta} | R Documentation |
For now, for details please see the vignette inst/script/linked.Rmd
makeLinkedTxome( indexDir, source, organism, release, genome, fasta, gtf, write = TRUE, jsonFile ) loadLinkedTxome(jsonFile)
indexDir |
the local path to the Salmon index |
source |
the source of transcriptome (e.g. "GENCODE", "Ensembl", "de-novo") |
organism |
organism (e.g. "Homo sapiens") |
release |
release number (e.g. "27") |
genome |
genome (e.g. "GRCh38", or "none") |
fasta |
location(s) for the FASTA transcript sequences (of which the transcripts used to build the index is equal or a subset). This can be a local path, or an HTTP or FTP URL |
gtf |
location for the GTF/GFF file
(of which the transcripts used to build the index is equal or a subset).
This can be a local path, or an HTTP or FTP URL
While the |
write |
logical, should a JSON file be written out which documents the transcriptome checksum and metadata? (default is TRUE) |
jsonFile |
the path to the json file for the linkedTxome |
nothing, the function is run for its side effects
# point to a Salmon quantification file with an additional artificial transcript dir <- system.file("extdata/salmon_dm", package="tximportData") file <- file.path(dir, "SRR1197474.plus", "quant.sf") coldata <- data.frame(files=file, names="SRR1197474", sample="1", stringsAsFactors=FALSE) # now point to the Salmon index itself to create a linkedTxome # as the index will not match a known txome indexDir <- file.path(dir, "Dm.BDGP6.22.98.plus_salmon-0.14.1") # point to the source FASTA and GTF: fastaFTP <- c("ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.22.cdna.all.fa.gz", "ftp://ftp.ensembl.org/pub/release-98/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.22.ncrna.fa.gz", "extra_transcript.fa.gz") gtfPath <- file.path(dir, "Drosophila_melanogaster.BDGP6.22.98.plus.gtf.gz") # now create a linkedTxome, linking the Salmon index to its FASTA and GTF sources makeLinkedTxome(indexDir=indexDir, source="Ensembl", organism="Drosophila melanogaster", release="98", genome="BDGP6.22", fasta=fastaFTP, gtf=gtfPath, write=FALSE) # to clear the entire linkedTxome table # (don't run unless you want to clear this table!) # bfcloc <- getTximetaBFC() # bfc <- BiocFileCache(bfcloc) # bfcremove(bfc, bfcquery(bfc, "linkedTxomeTbl")$rid)