aggregate: Aggregate Molecules into an Expression Matrix

aggregateR Documentation

Aggregate Molecules into an Expression Matrix


Aggregate Molecules into an Expression Matrix


## S3 method for class 'FOV'
aggregate(x, by = NULL, set = NULL, drop = TRUE, ...)

## S3 method for class 'Molecules'
aggregate(x, by, drop = TRUE, ...)



An object with spatially-resolved molecule information


Name of a Segmentation within object or a Segmentation object


Name of molecule set to aggregate


Drop molecules not present in a segmentation; if FALSE, adds a column called “boundless” consisting of molecule counts not in a segmentation


Arguments passed to other methods


An expression matrix

Progress Updates with progressr

This function uses progressr to render status updates and progress bars. To enable progress updates, wrap the function call in with_progress or run handlers(global = TRUE) before running this function. For more details about progressr, please read vignette("progressr-intro")

Parallelization with future

This function uses future to enable parallelization. Parallelization strategies can be set using plan. Common plans include “sequential” for non-parallelized processing or “multisession” for parallel evaluation using multiple R sessions; for other plans, see the “Implemented evaluation strategies” section of ?future::plan. For a more thorough introduction to future, see vignette("future-1-overview")

SeuratObject documentation built on May 29, 2024, 12:31 p.m.