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lgatto / pRoloc

A unifying bioinformatics framework for organelle proteomics
http://lgatto.github.io/pRoloc/
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Unexpected output from fDataToUnknown #144

Open lmsimp opened 2 years ago

lmsimp commented 2 years ago

Modify function to fix the below example

library(pRolocdata)
data("hyperLOPIT2015")
getMarkerClasses(hyperLOPIT2015)

hyperLOPIT2015 <- fDataToUnknown(hyperLOPIT2015, 
                                 fcol = "markers", 
                                 from = "Nucleus - Chromatin", 
                                 to = "CHROMATIN")
getMarkerClasses(hyperLOPIT2015)

hyperLOPIT2015 <- fDataToUnknown(hyperLOPIT2015, 
                                 fcol = "markers", 
                                 from = "Nucleus - Non-chromatin", 
                                 to = "NUCLEUS")
getMarkerClasses(hyperLOPIT2015)

hyperLOPIT2015 <- fDataToUnknown(hyperLOPIT2015, 
                                 fcol = "markers", 
                                 from = "NUCLEUS", 
                                 to = "NUCLEUS/CHROMATIN")
getMarkerClasses(hyperLOPIT2015)
 [1] "40S Ribosome"                          "60S Ribosome"                          "Actin cytoskeleton"                   
 [4] "CHROMATIN"                             "Cytosol"                               "Endoplasmic reticulum/Golgi apparatus"
 [7] "Endosome"                              "Extracellular matrix"                  "Lysosome"                             
[10] "Mitochondrion"                         "NUCLEUS/CHROMATIN"                     "Peroxisome"                           
[13] "Plasma membrane"                       "Proteasome"  

hyperLOPIT2015 <- fDataToUnknown(hyperLOPIT2015, 
                                 fcol = "markers", 
                                 from = "CHROMATIN", 
                                 to = "NUCLEUS/CHROMATIN")
getMarkerClasses(hyperLOPIT2015)
 [1] "40S Ribosome"                          "60S Ribosome"                          "Actin cytoskeleton"                   
 [4] "Cytosol"                               "Endoplasmic reticulum/Golgi apparatus" "Endosome"                             
 [7] "Extracellular matrix"                  "Lysosome"                              "Mitochondrion"                        
[10] "NUCLEUS/CHROMATIN"                     "NUCLEUS/NUCLEUS/CHROMATIN"             "Peroxisome"                           
[13] "Plasma membrane"                       "Proteasome"