scater (version 1.0.4)

readKallistoResults: Read kallisto results from a batch of jobs

Description

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

Usage

readKallistoResults(kallisto_log = NULL, samples = NULL, directories = NULL, read_h5 = FALSE, kallisto_version = "current", logExprsOffset = 1, verbose = TRUE)

Arguments

kallisto_log

list, generated by runKallisto. If provided, then samples and directories arguments are ignored.

samples

character vector providing a set of sample names to use for the abundance results.

directories

character vector providing a set of directories containing kallisto abundance results to be read in.

read_h5

logical, should the bootstrap results be read in from the HDF5 objects produced by kallisto?

kallisto_version

character string indicating whether or not the version of kallisto to be used is "pre-0.42.2" or "current". This is required because the kallisto developers changed the output file extensions and added features in version 0.42.2.

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?

Value

an SCESet object

Details

This function expects to find only one set of kallisto abundance results per directory; multiple adundance results in a given directory will be problematic.

Examples

## Not run: 
# kallisto_log <- runKallisto("targets.txt", "transcripts.idx", single_end=FALSE,
#          output_prefix="output", verbose=TRUE, n_bootstrap_samples=10)
# sceset <- readKallistoResults(kallisto_log)
# ## End(Not run)