scater (version 1.0.4)

readSalmonResults: Read Salmon results from a batch of jobs

Description

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

Usage

readSalmonResults(Salmon_log = NULL, samples = NULL, directories = NULL, logExprsOffset = 1, verbose = TRUE)

Arguments

Salmon_log

list, generated by runSalmon. 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 Salmon abundance results to be read in.

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 Salmon abundance results per directory; multiple adundance results in a given directory will be problematic.

Examples

## Not run: 
# ## Define output directories in a vector called here "Salmon_dirs"
# ## and sample names as "Salmon_samples"
# sceset <- readSalmonResults(samples = Salmon_samples, 
# directories = Salmon_dirs)
# ## End(Not run)