Worker function for calculating differentially abundant metabolites per pooling group.
This function is used by by FindAllDEMs().
Usage
run_DE(
pooled_data,
seurat_data,
ident,
output_dir,
run_name,
n,
logFC_threshold,
annotation.column,
assay,
return.individual = FALSE,
verbose = TRUE
)Arguments
- pooled_data
A SingleCellExperiment object which contains the pooled pseudo-replicate data.
- seurat_data
A Seurat object containing the merged Xenium data being analysed (this is subset).
- ident
A character string defining the ident column to perform differential expression analysis against.
- output_dir
A character string defining the ident column to perform differential expression analysis against.
- run_name
A character string defining the title of this DE analysis (will be used when saving DEMs to .csv file).
- n
An integer that defines the number of pseudo-replicates per sample (default = 3).
- logFC_threshold
A numeric value indicating the logFC threshold to use for defining significant genes (default = 1.2).
- annotation.column
Character string defining the column where annotation information is stored in the assay metadata. This requires AnnotateSeuratMALDI() to be run where the default column to store annotations is "all_IsomerNames" (default = "None").
- assay
A character string defining the assay where the mz count data and annotations are stored (default = "Spatial").
- return.individual
Boolean value defining whether to return a list of individual edgeR objects for each designated ident. If FALSE, one merged edgeR object will be returned (default = FALSE).
- 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 modified edgeR object which contains the relative pseudo-bulking analysis outputs, including a DEMs data.frame with a list of differential expressed m/z metabolites
Examples
utils::str(formals(run_DE))
#> Dotted pair list of 11
#> $ pooled_data : symbol
#> $ seurat_data : symbol
#> $ ident : symbol
#> $ output_dir : symbol
#> $ run_name : symbol
#> $ n : symbol
#> $ logFC_threshold : symbol
#> $ annotation.column: symbol
#> $ assay : symbol
#> $ return.individual: logi FALSE
#> $ verbose : logi TRUE
# pooled_obj <- run_pooling(SeuratObj, "sample", n = 3)
# run_DE(pooled_obj, SeuratObj, "sample", "~/Documents/DE_output/", "run_1", n = 3, logFC_threshold = 1.2, annotation.column = "all_IsomerNames", assay = "Spatial")