Calcuates the log-ratio of mean gene expression counts to mean negative probe counts.
Usage
getMeanSignalRatio(
seu_obj = NULL,
features = NULL,
platform = NULL,
expMat = "path_to_expMat"
)Arguments
- seu_obj
A Seurat object, expected to have both 'RNA' and 'ControlProbe' assays for calculating mean expression levels of genes and negative control probes, respectively.
- features
An optional vector of gene names for which to calculate the mean log-ratio. If NULL, the calculation is performed for all genes present in the 'RNA' assay of the seu_obj.
Value
A data frame with three columns: sample_id, platform, and value, where value represents the calculated
mean log-ratio of gene expression to negative control probe expression for the selected genes. This summary can be
used to assess the signal-to-noise ratio in the dataset.
Details
Computes the log-ratio of the mean expression levels of specified genes (or all genes if none are specified) to the mean expression levels of negative control probes within a Seurat object. This metric can provide insights into the overall signal strength relative to background noise levels.