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Merge Gene and Transcript Level Differential Expression Tables

Source: R/dea.R
join_DEG_DET.Rd

Table-based helper combining gene-level and transcript-level results into the long format used by plot_log2fc(). With an IsoformicExperiment, de_table() produces the same table from the stored results.

Usage

join_DEG_DET(
  deg_table,
  det_table,
  logfc_cut = 1,
  pval_cut = 0.05,
  use_fdr = FALSE,
  transcript_types = default_transcript_types()
)

Arguments

deg_table

Gene-level results with gene_id, gene_name, log2FC and pvalue columns.

det_table

Transcript-level results with transcript_id, transcript_name, transcript_type, log2FC and pvalue columns.

logfc_cut

Absolute log2 fold-change cutoff for significance.

pval_cut

P-value cutoff for significance. Like the cutoffs of de_tx(), a feature is significant when abs(log2FC) >= logfc_cut and the p-value is <= pval_cut.

use_fdr

Logical, test the qvalue column instead of pvalue (when present), as the stored cutoffs of an IsoformicExperiment do.

transcript_types

Transcript types to keep. NULL keeps all.

Value

A tibble with feature_id, feature_name, feature_type, gene_name, log2FC, pvalue (and qvalue when present) and is_de.

Examples

deg_table <- data.frame(
  gene_id = c("gene1", "gene2"),
  gene_name = c("GeneA", "GeneB"),
  log2FC = c(1.5, -2.0),
  pvalue = c(0.01, 0.04)
)
det_table <- data.frame(
  transcript_id = c("tx1", "tx2", "tx3"),
  transcript_name = c("Transcript1", "Transcript2", "Transcript3"),
  transcript_type = c("protein_coding", "lncRNA", "processed_transcript"),
  gene_name = c("GeneA", "GeneA", "GeneB"),
  log2FC = c(1.2, -1.8, 0.5),
  pvalue = c(0.02, 0.03, 0.2)
)
join_DEG_DET(deg_table, det_table, logfc_cut = 1, pval_cut = 0.05)
#> # A tibble: 5 × 8
#>   feature_id feature_name feature_type     gene_id gene_name log2FC pvalue is_de
#>   <chr>      <chr>        <chr>            <chr>   <chr>      <dbl>  <dbl> <chr>
#> 1 gene1      GeneA        gene             gene1   GeneA        1.5   0.01 yes  
#> 2 gene2      GeneB        gene             gene2   GeneB       -2     0.04 yes  
#> 3 tx1        Transcript1  protein_coding   NA      GeneA        1.2   0.02 yes  
#> 4 tx2        Transcript2  lncRNA           NA      GeneA       -1.8   0.03 yes  
#> 5 tx3        Transcript3  processed_trans… NA      GeneB        0.5   0.2  no