| 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 path to the Salmon or Sailfish index |
source |
the source of transcriptome (e.g. "Gencode" or "Ensembl") |
organism |
organism (e.g. "Homo sapiens") |
release |
release number (e.g. "27") |
genome |
genome (e.g. "GRCh38") |
fasta |
FTP location for the FASTA sequence (of which the index is a subset) |
gtf |
FTP location for the GTF file (of which the index is a subset) |
write |
should a JSON file be written out which documents the transcriptome signature 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 which combined two Ensembl FASTA files:
dir <- system.file("extdata/salmon_dm/SRR1197474", package="tximportData")
file <- file.path(dir, "quant.sf.gz")
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
dir <- system.file("extdata", package="tximeta")
indexDir <- file.path(dir, "Drosophila_melanogaster.BDGP6.v92_salmon_0.10.2")
# point to the source FASTA and GTF:
fastaFTP <- c("ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/cdna/Drosophila_melanogaster.BDGP6.cdna.all.fa.gz",
"ftp://ftp.ensembl.org/pub/release-92/fasta/drosophila_melanogaster/ncrna/Drosophila_melanogaster.BDGP6.ncrna.fa.gz")
# we comment this out for the example, and instead point to a local version
# usually one would point to the FTP source for the GTF file here
# gtfFTP <- "ftp://ftp.ensembl.org/pub/release-92/gtf/drosophila_melanogaster/Drosophila_melanogaster.BDGP6.92.gtf.gz"
dir2 <- system.file("extdata/salmon_dm", package="tximportData")
gtfPath <- file.path(dir2,"Drosophila_melanogaster.BDGP6.92.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="92", genome="BDGP6", 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)