Import counts

Import bcbio-rnaseq count data run using tximport

import_counts(bcbio, type = "salmon", grep = NULL, samples = NULL)

Arguments

bcbio

bcbio run object

type

The type of software used to generate the abundances. Follows the conventions of tximport().

grep

Apply grep pattern matching to sample names. This will override any parmeter set in samples.

samples

Specify the names of samples in bcbio final directory to input. If NULL (default), all samples will be imported.

Value

txi tximport list object

Examples

## Not run: ------------------------------------
# import_counts(bcbio, type = "salmon")
## ---------------------------------------------