linkedTxome {tximeta}R Documentation

Make and load linked transcriptomes ("linkedTxome")

Description

For now, for details please see the vignette inst/script/linked.Rmd

Usage

makeLinkedTxome(indexDir, source, organism, release, genome, fasta, gtf,
  write = TRUE, jsonFile)

loadLinkedTxome(jsonFile)

Arguments

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

Value

nothing, the function is run for its side effects

Examples


# 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)


[Package tximeta version 1.2.0 Index]