tests/testthat/_snaps/go.md

In CambridgeCentreForProteomics/camprotR: Processing, analysing and visualising CCP proteomics data

expand_terms() works

Code
  expand_terms(go_df = go_df, go_col = "GO.ID", go2Ancestor = go_2_ancestor)
Output
          GOID
  1 GO:0098808
  2 GO:0003723
  3 GO:0099568
  4 GO:0045087
  5       <NA>

get_enriched_go() works

Code
  lapply(out, class)
Output
  $category
  [1] "character"

  $over_represented_pvalue
  [1] "numeric"

  $under_represented_pvalue
  [1] "numeric"

  $numDEInCat
  [1] "integer"

  $numInCat
  [1] "integer"

  $term
  [1] "character"

  $ontology
  [1] "character"

  $over_represented_adj_pval
  [1] "numeric"

  $under_represented_adj_pval
  [1] "numeric"

  $term_short
  [1] "character"

estimate_go_overrep() works

Code
  lapply(out, class)
Output
  $category
  [1] "character"

  $over_represented_pvalue
  [1] "numeric"

  $under_represented_pvalue
  [1] "numeric"

  $numDEInCat
  [1] "integer"

  $numInCat
  [1] "integer"

  $term
  [1] "character"

  $ontology
  [1] "character"

  $over_represented_adj_pval
  [1] "numeric"

  $under_represented_adj_pval
  [1] "numeric"

  $term_short
  [1] "character"

  $adj_overrep
  [1] "numeric"

Code
  lapply(out2, class)
Output
  $category
  [1] "character"

  $over_represented_pvalue
  [1] "numeric"

  $under_represented_pvalue
  [1] "numeric"

  $numDEInCat
  [1] "integer"

  $numInCat
  [1] "integer"

  $term
  [1] "character"

  $ontology
  [1] "character"

  $over_represented_adj_pval
  [1] "numeric"

  $under_represented_adj_pval
  [1] "numeric"

  $term_short
  [1] "character"

  $adj_overrep
  [1] "numeric"

remove_redundant_go() works

Code
  lapply(out, class)
Output
  $category
  [1] "character"

  $over_represented_pvalue
  [1] "numeric"

  $under_represented_pvalue
  [1] "numeric"

  $numDEInCat
  [1] "integer"

  $numInCat
  [1] "integer"

  $term
  [1] "character"

  $ontology
  [1] "character"

  $over_represented_adj_pval
  [1] "numeric"

  $under_represented_adj_pval
  [1] "numeric"

  $term_short
  [1] "character"

  $adj_overrep
  [1] "numeric"

CambridgeCentreForProteomics/camprotR documentation built on July 7, 2024, 2:13 a.m.