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Differential Expression Results in an IsoformicExperiment

Source: R/dea.R
dea.Rd

An IsoformicExperiment stores differential expression results for transcripts (det) and genes (deg) in its dea property, together with the significance cutoffs used to flag features. Results can come from any tool: on assignment the tables are standardised to the column names log2FC, pvalue and qvalue (see Details), checked against the annotation, and stored as tibbles.

  • de_tx(x) / de_gene(x): results with an added det_sig / deg_sig column ("yes"/"no") computed from the cutoffs, sorted by absolute log2FC. Cutoffs can be overridden per call.

  • de_tx(x) <- value / de_gene(x) <- value: set results.

  • de_cutoffs(x) / de_cutoffs(x) <- value: the stored cutoffs, a list with log2fc (default 1), pvalue (default 0.05) and use_fdr (default TRUE, i.e. compare qvalue rather than pvalue).

  • de_table(x): a long table combining gene and transcript results, one row per feature, with feature_id, feature_name, feature_type ("gene" or the transcript type), gene_id, gene_name, log2FC, pvalue, qvalue and is_de. This is the input of plot_log2fc().

Usage

de_tx(
  self,
  log2fc_cutoff = NULL,
  pvalue_cutoff = NULL,
  use_fdr = NULL,
  sig_only = FALSE,
  ...
)

de_gene(
  self,
  log2fc_cutoff = NULL,
  pvalue_cutoff = NULL,
  use_fdr = NULL,
  sig_only = FALSE,
  ...
)

de_tx(self) <- value

de_gene(self) <- value

de_cutoffs(self, ...)

de_cutoffs(self) <- value

de_table(self, ...)

Arguments

self

An IsoformicExperiment.

log2fc_cutoff, pvalue_cutoff, use_fdr

Optional per-call overrides of the stored cutoffs.

sig_only

Logical, return only significant features.

...

Passed on to methods.

value

A data frame of results (de_tx<-, de_gene<-) or a list of cutoffs (de_cutoffs<-).

Value

Tibbles, or the modified object for replacement functions.

Details

Recognised column synonyms: log2FoldChange/logFC for log2FC; padj/FDR/adj.P.Val/svalue for qvalue; PValue/P.Value for pvalue. Row names are used as IDs when no ID column is present, and GENCODE-style |-suffixed transcript IDs are truncated. When qvalue is absent it is computed with Benjamini-Hochberg adjustment of pvalue.

Examples

iso <- example_isoformic()
de_cutoffs(iso)
#> $log2fc
#> [1] 1
#> 
#> $pvalue
#> [1] 0.05
#> 
#> $use_fdr
#> [1] TRUE
#> 
head(de_tx(iso))
#> # A tibble: 6 × 5
#>   transcript_id     log2FC      pvalue    qvalue det_sig
#>   <chr>              <dbl>       <dbl>     <dbl> <chr>  
#> 1 ENST00000638463.1   8.57 0.0226      0.102     no     
#> 2 ENST00000557508.5  -5.47 0.000000138 0.0000236 yes    
#> 3 ENST00000166139.9   5.01 0.000000138 0.0000236 yes    
#> 4 ENST00000592947.5   4.85 0.00000332  0.000211  yes    
#> 5 ENST00000508871.5  -4.61 0.0116      0.0658    no     
#> 6 ENST00000615840.4   3.82 0.000000138 0.0000236 yes    
head(de_gene(iso, sig_only = TRUE))
#> # A tibble: 6 × 8
#>   gene_id            log10mean  stat log2FC      pvalue   locfdr  qvalue deg_sig
#>   <chr>                  <dbl> <dbl>  <dbl>       <dbl>    <dbl>   <dbl> <chr>  
#> 1 ENSG00000070404.10      4.20  68     5.23 0.000000462  5.48e-5 2.58e-5 yes    
#> 2 ENSG00000130822.15      1.78  64.5   3.39 0.00000139   1.33e-4 4.69e-5 yes    
#> 3 ENSG00000102755.12      4.66  63.4   3.37 0.00000277   2.56e-4 8.56e-5 yes    
#> 4 ENSG00000070388.11      1.89  68.0   2.56 0.000000462  5.48e-5 2.58e-5 yes    
#> 5 ENSG00000061656.10      2.15  67.1   2.54 0.000000462  5.48e-5 2.58e-5 yes    
#> 6 ENSG00000106991.13      4.30  67     2.49 0.000000462  5.48e-5 2.58e-5 yes    
head(de_table(iso))
#> # A tibble: 6 × 9
#>   feature_id  feature_name feature_type gene_id gene_name log2FC  pvalue  qvalue
#>   <chr>       <chr>        <chr>        <chr>   <chr>      <dbl>   <dbl>   <dbl>
#> 1 ENSG000000… FSTL3        gene         ENSG00… FSTL3       5.23 4.62e-7 2.58e-5
#> 2 ENSG000001… PNCK         gene         ENSG00… PNCK        3.39 1.39e-6 4.69e-5
#> 3 ENSG000001… FLT1         gene         ENSG00… FLT1        3.37 2.77e-6 8.56e-5
#> 4 ENSG000000… FGF22        gene         ENSG00… FGF22       2.56 4.62e-7 2.58e-5
#> 5 ENSG000000… SPAG4        gene         ENSG00… SPAG4       2.54 4.62e-7 2.58e-5
#> 6 ENSG000001… ENG          gene         ENSG00… ENG         2.49 4.62e-7 2.58e-5
#> # ℹ 1 more variable: is_de <chr>

de_cutoffs(iso) <- list(log2fc = 0.5)
sum(de_tx(iso)$det_sig == "yes")
#> [1] 135