subset_expt: Extract a subset of samples following some rule(s) from an...

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

Extract a subset of samples following some rule(s) from an experiment class.

Description

Sometimes an experiment has too many parts to work with conveniently, this operation allows one to break it into smaller pieces.

Usage

subset_expt(
  expt,
  subset = NULL,
  ids = NULL,
  nonzero = NULL,
  coverage = NULL,
  print_excluded = TRUE
)

Arguments

expt	Expt chosen to extract a subset of data.
subset	Valid R expression which defines a subset of the design to keep.
ids	List of sample IDs to extract.
nonzero	Look for a minimal number of nonzero genes.
coverage	Request a minimum coverage/sample rather than text-based subset.
print_excluded	Print out the samples which are removed via this filter?

Value

metadata Expt class which contains the smaller set of data.

See Also

[Biobase] [pData()] [exprs()] [fData()]

Examples

## Not run: 
 smaller_expt <- expt_subset(big_expt, "condition=='control'")
 all_expt <- expt_subset(expressionset, "")  ## extracts everything

## End(Not run)

elsayed-lab/hpgltools documentation built on May 9, 2024, 5:02 a.m.