R: Aggregate Molecules into an Expression Matrix

aggregate {SeuratObject} | R Documentation

## Aggregate Molecules into an Expression Matrix

### Description

Aggregate Molecules into an Expression Matrix

### Usage

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

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

### Arguments

`x` | An object with spatially-resolved molecule information
`by` | Name of a `Segmentation` within `object` or a `Segmentation` object
`set` | Name of molecule set to aggregate
`drop` | 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

### Value

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")`

[Package SeuratObject version 4.1.0 Index]