GetUpdateStats: Gene Symbol Update Statistics

In vertesy/Seurat.utils: Seurat.utils - utility functions for Seurat

Gene Symbol Update Statistics

Description

Generates statistics on the gene symbol updates performed by UpdateGenesSeurat(). This function analyzes the data frame of gene symbols before and after the update process, providing insights into the proportion and total number of genes that were updated.

Usage

GetUpdateStats(genes = HGNC.updated[[i]])

Arguments

genes

A data frame of gene symbols before and after update, typically the output of UpdateGenesSeurat(). Default: HGNC.updated[[i]] (where i is the index of the desired Seurat object in a list).

Details

The function examines the Approved column of the input data frame to identify gene symbols marked for update and compares the original and suggested symbols to determine actual updates. The statistics highlight the efficiency and impact of the gene symbol updating process, aiding in the assessment of data preprocessing steps.

Value

A named vector with statistics on gene updates, including the percentage of updated genes, the absolute number of updated genes, and the total number of genes processed.

Note

The function requires the input data frame to have specific columns as produced by HGNChelper::checkGeneSymbols() and subsequently processed by UpdateGenesSeurat(). Ensure that the input adheres to this format for accurate statistics.

See Also

UpdateGenesSeurat, for the function that updates gene symbols and produces the input data frame for this function.

Examples

## Not run: 
if (interactive()) {
  # Assuming `HGNC.updated.genes` is your data frame containing the original and
  # suggested gene symbols, as returned by `UpdateGenesSeurat()`
  updateStats <- GetUpdateStats(genes = HGNC.updated.genes)
  # `updateStats` now contains the update statistics, including percentage and count of updated genes
}

## End(Not run)

vertesy/Seurat.utils documentation built on Dec. 4, 2024, 5:20 p.m.