tximeta: tximeta: Transcript quantification import with automatic...
In tximeta: Transcript Quantification Import with Automatic Metadata

Description Usage Arguments Details Value Examples

tximeta leverages the hashed checksum of the Salmon 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. Note that tximeta requires that the entire output directory of Salmon or alevin is present and unmodified in order to identify the provenance of the reference transcripts.

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

`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).
`...`	arguments passed to `tximport`

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 checksum 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 checksum 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).

a SummarizedExperiment with metadata on the rowRanges. (if the hashed checksum 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)

# 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="Ensembl", 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)