It calculated mean expression per probe.
Usage
getMeanExpression(
seu_obj = NULL,
features = NULL,
expMat = "path_to_expMatrix",
platform = NULL
)Arguments
- seu_obj
A Seurat object. This object must have an RNA assay for target genes and a ControlProbe assay for control probes.
- features
An optional vector of gene names for which to calculate mean expression. If NULL, mean expression is calculated for all genes in the RNA assay.
- expMat
Path to exprMatrix file.
- platform
The platform from which the data originates. Valid options are 'Xenium', 'CosMx', and 'Merscope'.
Value
A data frame with columns target (gene or control probe name), value (mean expression level),
type (indicating whether the row represents a Gene or Control), platform, and sample_id.
Details
Computes the mean expression levels for a specified list of features (genes) and control probes within a Seurat object. This function separately calculates the mean expression for both target genes and control probes, then combines these results into a single data frame. If no features are specified, it defaults to all genes in the RNA assay.