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Read Salmon Quantifications Into an IsoformicExperiment

Source: R/read_salmon.R
read_salmon.Rd

Reads quant.sf files produced by Salmon (salmon quant) directly with DuckDB, without going through tximport, and returns an IsoformicExperiment with transcript-level abundance (TPM), counts (NumReads) and length (EffectiveLength) assays. Gene-level assays are derived lazily by the object (see gene_assays()).

Usage

read_salmon(
  paths,
  annot_path,
  col_data = NULL,
  experiment_name = NULL,
  ignore_after_bar = TRUE,
  drop_unannotated = FALSE,
  inferential = FALSE
)

Arguments

paths

Character vector of Salmon output directories (containing quant.sf) or paths to quant.sf files. Names, when present, are used as sample IDs; otherwise the directory name is used.

annot_path

Annotation directory or GFF3/GTF file (see prepare_isoformic_annotation()).

col_data

Optional data frame of sample metadata whose first column (or a sample_id column) matches the sample IDs. When NULL, a minimal table with just sample_id is created.

experiment_name

Optional experiment name.

ignore_after_bar

Logical. Keep only the part of transcript names before the first | (GENCODE FASTA headers used as Salmon references).

drop_unannotated

Logical. Drop transcripts absent from the annotation (with a message) instead of failing.

inferential

Logical. Read the inferential replicates, equivalence classes and run metadata of the Salmon directories and compute the uncertainty tables with add_uncertainty() (default settings; call that function for other cutoffs or a contrast). The directories must have been quantified with --numGibbsSamples or --numBootstraps.

Value

An IsoformicExperiment.

Details

All files are read in one DuckDB query and pivoted to wide matrices, so reading tens of samples with 200,000 transcripts each takes seconds. Inferential replicates (Gibbs/bootstrap samples) are read only with inferential = TRUE, which also computes the uncertainty tables of add_uncertainty(); for swish they are imported with tximeta/fishpond and converted with as_isoformic().

Examples

quant_dirs <- list.files(
  system.file("extdata", "mini_quants", package = "isoformic"),
  full.names = TRUE
)
names(quant_dirs) <- sub("_quant$", "", basename(quant_dirs))
annot <- system.file("extdata", "mini_annotation", package = "isoformic")
iso <- read_salmon(quant_dirs, annot_path = annot)
iso
#> <IsoformicExperiment> isoformic_2da713f64b
#>   annotation : gencode_v49_mini_subset (15 genes, 111 transcripts, 1,071 exons)
#>   samples    : 6
#>   transcripts: 111 assayed from 15 genes
#>   assays     : abundance, counts, length
#>   gene assays: derived from transcript assays on demand
#>   DE results : <none>