readKallisto {SummarizedExperiment} | R Documentation

## Input kallisto or kallisto bootstrap results.

### Description

WARNING: `readKallisto()` is deprecated. Please use `tximeta()` from the tximeta package instead.

`readKallisto` inputs several kallisto output files into a single `SummarizedExperiment` instance, with rows corresponding to estimated transcript abundance and columns to samples. `readKallistoBootstrap` inputs kallisto bootstrap replicates of a single sample into a matrix of transcript x bootstrap abundance estimates.

### Usage

    readKallisto(files,
        json = file.path(dirname(files), "run_info.json"),
        h5 = any(grepl("\\.h5$", files)), what = KALLISTO_ASSAYS,
        as = c("SummarizedExperiment", "list", "matrix"))

    readKallistoBootstrap(file, i, j)

### Arguments

`files` | character() paths to kallisto ‘abundance.tsv’ output files. The assumption is that files are organized in the way implied by kallisto, with each sample in a distinct directory, and the directory containing files abundance.tsv, run_info.json, and perhaps abundance.h5.
`json` | character() vector of the same length as `files` specifying the location of JSON files produced by kallisto and containing information on the run. The default assumes that json files are in the same directory as the corresponding abundance file.
`h5` | character() vector of the same length as `files` specifying the location of HDF5 files produced by kallisto and containing bootstrap estimates. The default assumes that HDF5 files are in the same directory as the corresponding abundance file.
`what` | character() vector of kallisto per-sample outputs to be input. See KALLISTO_ASSAYS for available values.
`as` | character(1) specifying the output format. See `Value` for additional detail.
`file` | character(1) path to a single HDF5 output file.
`i, j` | integer() vector of row (`i`) and column (`j`) indexes to input.

### Value

A `SummarizedExperiment`, `list`, or `matrix`, depending on the value of argument `as`; by default a `SummarizedExperiment`. The `as="SummarizedExperiment"` `rowData(se)` the length of each transcript; `colData(se)` includes summary information on each sample, including the number of targets and bootstraps, the kallisto and index version, the start time and operating system call used to create the file. `assays()` contains one or more transcript x sample matrices of parameters estimated by kallisto (see `KALLISTO_ASSAYS`).

`as="list"` return value contains information simillar to `SummarizedExperiment` with row, column and assay data as elements of the list without coordination of row and column annotations into an integrated data container. `as="matrix"` returns the specified assay as a simple R matrix.

### Author(s)

Martin Morgan martin.morgan@roswellpark.org

### References

http://pachterlab.github.io/kallisto software for quantifying transcript abundance.

### Examples

    ## Not run:
    outputs <- system.file(package="SummarizedExperiment", "extdata",
        "kallisto")
    files <- dir(outputs, pattern="abundance.tsv", full=TRUE, recursive=TRUE)
    stopifnot(all(file.exists(files)))

    ## default: input 'est_counts'
    (se <- readKallisto(files, as="SummarizedExperiment"))
    str(readKallisto(files, as="list"))
    str(readKallisto(files, as="matrix"))

    ## available assays
    KALLISTO_ASSAYS
    ## one or more assay
    readKallisto(files, what=c("tpm", "eff_length"))

    ## alternatively: read hdf5 files
    files <- sub(".tsv", ".h5", files, fixed=TRUE)
    readKallisto(files)

    ## input all bootstraps
    xx <- readKallistoBootstrap(files[1])
    ridx <- head(which(rowSums(xx) != 0), 3)
    cidx <- c(1:5, 96:100)
    xx[ridx, cidx]

    ## selective input of rows (transcripts) and/or bootstraps
    readKallistoBootstrap(files[1], i=c(ridx, rev(ridx)), j=cidx)

    ## End(Not run)

[Package SummarizedExperiment version 1.24.0 Index]