Pools SpaMTP Seurat object into random pools for pseudo-bulking.

Runs pooling of a SpaMTP dataset to generate pseudo-replicates for each unique identity provided. This function is used by FindAllDEMs().

Usage

run_pooling(data.filt, idents, n, assay, slot, verbose = TRUE)

Arguments

data.filt

A Seurat Object containing count values for pooling.

idents

A character string defining the idents column to pool the data against.

n

An integer defining the amount of pseudo-replicates to generate for each sample (default = 3).

assay

Character string defining the assay where the mz count data and annotations are stored (default = "Spatial").

slot

Character string defining the assay storage slot to pull the relative mz intensity values from (default = "counts").

verbose

Boolean indicating whether to show the message. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

Value

A SinglCellExpereiment object which contains pooled (n)-pseudo-replicate counts data based on the Seurat Object input

Examples

# run_pooling <- list(seuratObj, idents = "sample", n = 3, assay = "Spatial", slot = "counts")