tests/testthat/test-selectProtein.R

In kairenchen721/interpretproteinidentification: Visually Interprets Protein Identification

test_that("select protein works", {
  allEdges <- c(
    "SHC(Carbamidomethyl)IAEVEK",
    "P02769",
    "LAMTLAEAER",
    "A9GID7",
    "KSDDGGEVEK",
    "A9G8G1",
    "LAMTLAEAER",
    "A9GID7",
    "YIC(Carbamidomethyl)DNQDTISSK",
    "P02769",
    "DDSPDLPK",
    "P02769",
    "C(Carbamidomethyl)C(Carbamidomethyl)TESLVNR",
    "P02769",
    "EC(Carbamidomethyl)C(Carbamidomethyl)DKPLLEK",
    "P02769", 
    "LALDLVVR",
    "A9GN44",
    "LC(Carbamidomethyl)VLHEK",
    "P02769",
    "C(Carbamidomethyl)C(Carbamidomethyl)TESLVNR",
    "P02769",
    "EC(Carbamidomethyl)C(Carbamidomethyl)DKPLLEK",
    "P02769",
    "LC(Carbamidomethyl)VLHEK",
    "P02769",
    "YIC(Carbamidomethyl)DNQDTISSK",
    "P02769",
    "EC(Carbamidomethyl)C(Carbamidomethyl)DKPLLEK",
    "P02769",
    "DLGEEHFK",
    "P02769",
    "DLGEEHFK",
    "P02769",
    "GM(Oxidation)LWAVFEQK",
    "A9GV08",
    "DLGEEHFK",
    "P02769",
    "YIC(Carbamidomethyl)DNQDTISSK",                
    "P02769",
    "LVTDLTK",
    "P02769",
    "DLGEEHFK",
    "P02769",
    "LC(Carbamidomethyl)VLHEK",
    "P02769",
    "LC(Carbamidomethyl)VLHEK",
    "P02769",
    "LAADDFR",
    "Q14532",
    "LAADDFR",
    "O76014",
    "LAADDFR",
    "O76015",
    "LAADDFR",
    "O76013",
    "LAADDFR",
    "Q92764",
    "LAADDFR",
    "Q15323",
    "LAADDFR",
    "Q14525",
    "GAC(Carbamidomethyl)LLPK",
    "P02769",
    "DLGEEHFK",
    "P02769",
    "AEFVEVTK",                                     
    "P02769",
    "GAC(Carbamidomethyl)LLPK",
    "P02769",
    "AEFVEVTK",
    "P02769",
    "EAC(Carbamidomethyl)FAVEGPK",
    "P02769",
    "GAC(Carbamidomethyl)LLPK",
    "P02769",
    "AGAFSLPK",
    "A9G0B6",
    "VATVSLPR",                                     
    "P00761",
    "EAC(Carbamidomethyl)FAVEGPK",
    "P02769",
    "AGDLLFFK",
    "A9FUD7",
    "HLVDEPQNLIK",
    "P02769",
    "YLYEIAR",
    "P02769",
    "YLYEIAR",
    "P02769",
    "YLYEIAR",
    "P02769",
    "LVVSTQTALA",
    "P02769",
    "HLVDEPQNLIK",                                  
    "P02769",
    "HLVDEPQNLIK",
    "P02769",
    "LKPDPNTLC(Carbamidomethyl)DEFK",
    "P02769"
  )
  
  myProteins <- c(
    "SHC(Carbamidomethyl)IAEVEK",
    "P02769",                           
    "YIC(Carbamidomethyl)DNQDTISSK",                
    "DDSPDLPK",                                    
    "C(Carbamidomethyl)C(Carbamidomethyl)TESLVNR",  
    "EC(Carbamidomethyl)C(Carbamidomethyl)DKPLLEK",
    "LC(Carbamidomethyl)VLHEK",                     
    "DLGEEHFK",                                    
    "LVTDLTK",                                      
    "GAC(Carbamidomethyl)LLPK",                    
    "AEFVEVTK",                                     
    "EAC(Carbamidomethyl)FAVEGPK",                 
    "HLVDEPQNLIK",                                  
    "YLYEIAR",                                     
    "LVVSTQTALA",                                   
    "LKPDPNTLC(Carbamidomethyl)DEFK"   
  )
  handMadeGraph <- igraph::make_graph(myProteins, directed = FALSE)
  handMadeGraph <- igraph::simplify(handMadeGraph)
  
  generatedGraphComponents <- 
    interpretproteinidentification::generateBipartiteGraph(allEdges, "")
  component <- interpretproteinidentification::displayComponent(
    generatedGraphComponents, 1
  )
  generatedSubGraph <- 
    interpretproteinidentification::selectProtein(component,
                                                  "P02769")$graph
  expect_equal(igraph::V(generatedSubGraph)$name, igraph::V(handMadeGraph)$name)
})

# [END]