tximeta: Import transcript quantification with metadata

In mikelove/tximeta: Transcript Quantification Import with Automatic Metadata

Import transcript quantification with metadata

Description

tximeta leverages the hashed digest of the Salmon or piscem index, in addition to a number of core Bioconductor packages (GenomicFeatures, ensembldb, AnnotationHub, GenomeInfoDb, BiocFileCache) to automatically populate metadata for the user, without additional effort from the user. For other quantifiers see the customMetaInfo argument below.

Usage

tximeta(
  coldata,
  type = NULL,
  txOut = TRUE,
  skipMeta = FALSE,
  skipSeqinfo = FALSE,
  useHub = TRUE,
  markDuplicateTxps = FALSE,
  cleanDuplicateTxps = FALSE,
  customMetaInfo = NULL,
  skipFtp = FALSE,
  ...
)

Arguments

coldata	a data.frame with at least two columns (others will propogate to object): files - character, paths of quantification files names - character, sample names if coldata is a vector, it is assumed to be the paths of quantification files and unique sample names are created
type	what quantifier was used (see tximport)
txOut	whether to output transcript-level data. tximeta is designed to have transcript-level output with Salmon, so default is TRUE, and it's recommended to use summarizeToGene following tximeta for gene-level summarization. For an alevin file, tximeta will import the gene level counts ignoring this argument (alevin produces only gene-level quantification).
skipMeta	whether to skip metadata generation (e.g. to avoid errors if not connected to internet). This calls tximport directly and so either txOut=TRUE or tx2gene should be specified.
skipSeqinfo	whether to skip the addition of Seqinfo, which requires an internet connection to download the relevant chromosome information table from UCSC
useHub	whether to first attempt to download a TxDb/EnsDb object from AnnotationHub, rather than creating from a GTF file from FTP (default is TRUE). If FALSE, it will force tximeta to download and parse the GTF
markDuplicateTxps	whether to mark the status (hasDuplicate) and names of duplicate transcripts (duplicates) in the rowData of the SummarizedExperiment output. Subsequent summarization to gene level will keep track of the number of transcripts sets per gene (numDupSets)
cleanDuplicateTxps	whether to try to clean duplicate transcripts (exact sequence duplicates) by replacing the transcript names that do not appear in the GTF with those that do appear in the GTF
customMetaInfo	the relative path to a custom metadata information JSON file, relative to the paths in files of coldata. For example, customMetaInfo="meta_info.json" would indicate that in the same directory as the quantification files in files, there are custom metadata information JSON files. These should contain the SHA-256 hash of the reference transcripts with the index_seq_hash tag (see details in vignette).
skipFtp	whether to avoid ftp:// in case of firewall, default is FALSE
...	arguments passed to tximport

Details

Most of the code in tximeta works to add metadata and transcript ranges when the quantification was performed with Salmon. However, tximeta can be used with any quantification type that is supported by tximport, where it will return an non-ranged SummarizedExperiment.

tximeta performs a lookup of the hashed digest of the index (stored in an auxilary information directory of the Salmon output) against a database of known transcriptomes, which lives within the tximeta package and is continually updated on Bioconductor's release schedule. In addition, tximeta performs a lookup of the digest against a locally stored table of linkedTxome's (see link{makeLinkedTxome}). If tximeta detects a match, it will automatically populate, e.g. the transcript locations, the transcriptome release, the genome with correct chromosome lengths, etc. It allows for automatic and correct summarization of transcript-level quantifications to the gene-level via summarizeToGene without the need to manually build a tx2gene table.

tximeta on the first run will ask where the BiocFileCache for this package should be kept, either using a default location or a temporary directory. At any point, the user can specify a location using setTximetaBFC and this choice will be saved for future sessions. Multiple users can point to the same BiocFileCache, such that transcript databases (TxDb or EnsDb) associated with certain Salmon indices and linkedTxomes can be accessed by different users without additional effort or time spent downloading and building the relevant TxDb / EnsDb. Note that, if the TxDb or EnsDb is present in AnnotationHub, tximeta will use this object instead of downloading and building a TxDb/EnsDb from GTF (to disable this set useHub=FALSE).

In order to allow that multiple users can read and write to the same location, one should set the BiocFileCache directory to have group write permissions (g+w).

Value

a SummarizedExperiment with metadata on the rowRanges. (if the hashed digest in the Salmon or Sailfish index does not match any known transcriptomes, or any locally saved linkedTxome, tximeta will just return a non-ranged SummarizedExperiment)

Examples

# point to a Salmon quantification file:
dir <- system.file("extdata/salmon_dm", package="tximportData")
files <- file.path(dir, "SRR1197474", "quant.sf") 
coldata <- data.frame(files, names="SRR1197474", condition="A", stringsAsFactors=FALSE)

# normally we would just run the following which would download the appropriate metadata
# se <- tximeta(coldata)

# for this example, we instead point to a local path where the GTF can be found
# by making a linkedTxome:
indexDir <- file.path(dir, "Dm.BDGP6.22.98_salmon-0.14.1")
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")
gtfPath <- file.path(dir, "Drosophila_melanogaster.BDGP6.22.98.gtf.gz")
makeLinkedTxome(indexDir=indexDir, source="LocalEnsembl", organism="Drosophila melanogaster",
                release="98", genome="BDGP6.22", fasta=fastaFTP, gtf=gtfPath, write=FALSE)
se <- tximeta(coldata)

# 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)

mikelove/tximeta documentation built on Oct. 21, 2024, 5:46 a.m.