readTxResults {scater} | R Documentation

## Read transcript quantification data with tximport package

### Description

After generating transcript/feature abundance results using kallisto, Salmon, Sailfish or RSEM for a batch of samples, read these abundance values into an `SCESet` object.

### Usage

    readTxResults(samples = NULL, files = NULL, log = NULL,
      type = "kallisto", txOut = TRUE, logExprsOffset = 1, verbose = TRUE,
      ...)

### Arguments

`samples` | character vector providing a set of sample names to use for the abundance results.
`files` | character vector providing a set of filenames containing kallisto abundance results to be read in.
`log` | list (optional), generated by `runKallisto`. If provided, then `samples` and `files` arguments are ignored.
`type` | character, the type of software used to generate the abundances. Options are "kallisto", "salmon", "sailfish", "rsem". This argument is passed to `tximport`.
`txOut` | logical, whether the function should just output transcript-level (default TRUE)
`logExprsOffset` | numeric scalar, providing the offset used when doing log2-transformations of expression data to avoid trying to take logs of zero. Default offset value is `1`.
`verbose` | logical, should function provide output about progress?
`...` | optional parameters passed to `tximport`. See documentation for `tximport` for options and details.

### Details

Note: tximport does not import bootstrap estimates from kallisto, Salmon, or Sailfish. If you want bootstrap estimates use the `readKallistoResults` or `readSalmonResults` functions.

### Value

an `SCESet` object containing the abundance, count and feature length data from the supplied samples.

### References

Soneson C, Love MI, Robinson MD. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res. 2015;4: 1521.

### Examples

    ## Not run:
    ## this example requires installation of the tximportData package from
    ## Bioconductor
    library(tximportData)
    dir <- system.file("extdata", package = "tximportData")
    list.files(dir)
    samples <- read.table(file.path(dir, "samples.txt"), header = TRUE)
    samples
    directories <- file.path(dir, "kallisto", samples$run)
    names(directories) <- paste0("sample", 1:6)
    files <- file.path(directories, "abundance.tsv")
    sce_example <- readTxResults(samples = names(directories),
    files = files, type = "kallisto")

    ## for faster reading of results use the read_tsv function from the readr pkg
    library(readr)
    sce_example <- readTxResults(samples = names(directories),
    files = files, type = "kallisto", reader = read_tsv)

    ## End(Not run)

[Package scater version 1.6.3 Index]