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