Finds differentially expressed m/z values/metabolites between all comparison groups.
Source:R/DifferentialMZPeaks.R
FindAllDEMs.RdFinds differentially expressed m/z values/metabolites between all comparison groups.
Usage
FindAllDEMs(
data,
ident,
n = 3,
logFC_threshold = 1.2,
DE_output_dir = NULL,
run_name = "FindAllDEMs",
annotation.column = NULL,
assay = "Spatial",
slot = "counts",
return.individual = FALSE,
verbose = TRUE
)Arguments
- data
A Seurat object containing mz values for differential expression analysis.
- ident
A character string defining the metadata column or groups to compare mz values between.
- n
An integer that defines the number of pseudo-replicates (pools) per sample (default = 3).
- logFC_threshold
A numeric value indicating the logFC threshold to use for defining significant genes (default = 1.2).
- DE_output_dir
A character string defining the directory path for all output files to be stored. This path must a new directory. Else, set to NULL as default.
- run_name
A character string defining the title of this DE analysis that will be used when saving DEMs to .csv file (default = 'FindAllDEMs').
- 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").
- slot
Character string defining the assay storage slot to pull the relative mz intensity values from. Note: EdgeR requires raw counts, all values must be positive (default = "counts").
- 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).