myTAI (version 2.3.4)

genes_top_expr: Gene Expression Filtering Functions

Description

Collection of functions for filtering genes based on expression patterns in PhyloExpressionSet objects.

Generic function to select genes with the highest values for a given expression metric.

Usage

genes_top_expr(phyex_set, FUN = rowMeans, top_p = 0.99, top_k = NULL, ...)

Value

Character vector of gene IDs with metric values >= top_p quantile or top top_k genes

Arguments

phyex_set

A PhyloExpressionSet object

FUN

Function to calculate gene-wise expression metric (default: rowMeans)

top_p

Quantile threshold for gene selection (default: 0.99). Ignored if top_k is specified.

top_k

Absolute number of top genes to select (default: NULL). Takes precedence over top_p.

...

Additional arguments passed to FUN

Details

This function applies the specified function to calculate a metric for each gene across samples, then selects genes above the specified quantile threshold or the top k genes by absolute count. If both top_p and top_k are specified, top_k takes precedence.

Examples

# Select top 1% most expressed genes by mean
high_expr_genes <- genes_top_expr(example_phyex_set, function(x) apply(x, 1, mean), top_p = 0.99)

# Select top 100 most expressed genes
top_100_genes <- genes_top_expr(example_phyex_set, function(x) apply(x, 1, mean), top_k = 100)