sample: Sample selects replicates across specified plates.

In cytomining/cytotools: Command-Line Tools to Get Things Done Using Cytominer

Sample selects replicates across specified plates.

Description

sample replicates across specified plates, and aggregates the result in a single file. It assumes the following files exist:

• <workspace_dir>/metadata/barcode_platemap.csv which maps the plate barcodes to the corresponding platemaps,

• For each plate barcode, a CSV file <workspace_dir>/backend/<batch_id>/<file-matching-specified-pattern> which will be among the files included in the sample.

Usage

sample(batch_id, pattern, output, replicates = NULL, workspace_dir = ".")

Arguments

batch_id	Batch ID.
pattern	Regular expression specifying the filenames containing the profiles from which to sample. Only CSVs are allowed.
output	Output file. The extension should be either csv, rds, or feather.
replicates	Number of replicates to select per plate map. Selects all replicates if NULL. default: NULL.
workspace_dir	Root directory containing backend and metadata subdirectories. Can be relative or absolute. default: ".".

cytomining/cytotools documentation built on Sept. 18, 2024, 11:58 p.m.