SummarizedExperiment (version 1.2.3)

readKallisto: Input kallisto or kallisto bootstrap results.

Description

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.

References

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

Examples

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)