getTxPerCell

Calculate the average number of transcripts per cell for the given features.

Usage

getTxPerCell(
  seu_obj = NULL,
  features = NULL,
  expMat = "path_to_exprMatrix",
  platform
)

Arguments

seu_obj

A Seurat object with RNA assays. The object must have 'sample_id' and 'platform' metadata attributes for identification and reporting purposes.

features

An optional vector of feature names (e.g., gene symbols) to include in the calculation. Defaults to NULL, in which case the calculation uses all available features in the RNA assay of the Seurat object.

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 'sample_id', 'platform', and 'value', where 'value' represents the mean number of transcripts per cell calculated across the specified features. This output can be useful for comparative analysis across samples or experimental conditions.

Details

This function calculates the mean number of transcripts per cell for a specified set of features (genes) in a Seurat object. If no features are specified, the function defaults to using all targets available within the RNA assay of the provided Seurat object. It's a useful metric for assessing the overall transcriptional activity within the sampled cells.