getAllMetrics

Compute various metrics for a given set of samples

Usage

getAllMetrics(df_samples, features = NULL)

Arguments

df_samples

A data.frame that must contain the following columns:

• sample_idUnique identifier for each sample.

• platformThe platform used, either "Xenium" or "CosMx".

• expMatPath to the expression matrix file. For Xenium platform, this should be a path to the cell_feature_matrix folder.

• tx_filePath to the transcript file.

• cell_metaPath to the cell metadata file.

Value

A modified version of df_samples with the computed metrics added as new columns.

Details

Computes various metrics for spatial transcriptomic data for a given set of samples. This function processes a data.frame containing sample information, including paths to necessary files, to compute a variety of metrics for each sample. The metrics outputted include the number of cells, specificity FDR, number of transcripts per cell, transcripts per area of segmented cell, transcripts per nucleus, signal to noise ratio, fraction of transcripts in segmented cells, Mutually Exclusive Co-Expression Rate (MECR), sparsity, and Shannon entropy. To initiate vignette, the data frame must include the columns: sample_id, platform, expMat, tx_file, and cell_meta.