Get expressed genes/loci by FDR

A method to filter genes or loci that are considered 'expressed' in a specific condition, based on a False Discovery Rate (FDR) threshold. The method is a wrapper around the filter_genes_by_fdr function.

Usage

expressed(object, condition, fdr = 0.05, which = "any")

Arguments

object

A DamIDResults object. This object must have been generated from data loaded with load_data_genes(calculate_occupancy_pvals = TRUE) for the underlying FDR columns to be present.

condition

A character string identifying the experimental condition to filter. This can be the internal identifier or the user-friendly display name.

fdr

Numeric. The FDR cutoff. Defaults to 0.05.

which

Character string, either 'any' or 'all'. Determines whether a gene must pass the FDR threshold in any or all replicates of the condition. Defaults to 'any'.

Value

A data.frame containing the gene_name and gene_id of genes that pass the filter.

See also

filter_genes_by_fdr, DamIDResults-class, load_data_genes

Examples

.generate_fdr_example_results <- function() {
    occupancy_df <- data.frame(
        gene_name = c("geneA", "geneB", "geneC"),
        gene_id = c("FBgn01", "FBgn02", "FBgn03"),
        L4_rep1 = c(1.5, 0.2, 0.8),
        L4_rep2 = c(1.7, 0.9, 0.1),
        L5_rep1 = c(0.1, 0.1, 2.0),
        L4_rep1_FDR = c(0.01, 0.10, 0.04),
        L4_rep2_FDR = c(0.03, 0.02, 0.50),
        L5_rep1_FDR = c(0.80, 0.90, 0.01),
        row.names = c("geneA", "geneB", "geneC")
    )
    diff_results_base <- list(
        occupancy = occupancy_df,
        test_category = "expressed",
        matched_samples = list("L4" = c("L4_rep1", "L4_rep2"), "L5" = "L5_rep1")
    )
    new("DamIDResults",
        analysis = data.frame(row.names = rownames(occupancy_df)),
        upCond1 = data.frame(),
        upCond2 = data.frame(),
        cond = c("L4 mock" = "L4", "L5 mock" = "L5"),
        data = diff_results_base
    )
}
mock_fdr_results <- .generate_fdr_example_results()

# Get expressed in a condition (FDR <= 0.05)
expressed(mock_fdr_results, condition = "L4 mock")
#> 3 genes passed the FDR filter using rule 'any'.
#>       gene_name gene_id avg_occ fdr_val
#> geneA     geneA  FBgn01    1.60    0.01
#> geneB     geneB  FBgn02    0.55    0.02
#> geneC     geneC  FBgn03    0.45    0.04

# Get genes expressed with a more stringent FDR (<= 0.01)
expressed(mock_fdr_results, condition = "L4", fdr = 0.01)
#> 1 genes passed the FDR filter using rule 'any'.
#>       gene_name gene_id avg_occ fdr_val
#> geneA     geneA  FBgn01     1.6    0.01