Skip to content

Instantly share code, notes, and snippets.

@dfjenkins3

dfjenkins3/compare_tggates_drugmatrix.md

Created December 17, 2015 20:44
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save dfjenkins3/b91d8230f248fa296b24 to your computer and use it in GitHub Desktop.
Save dfjenkins3/b91d8230f248fa296b24 to your computer and use it in GitHub Desktop.
Download ZIP
Comparing GenTox with Bacterial.Mutagenesis
Raw
compare_tggates_drugmatrix.md

Comparing GenTox with Bacterial.Mutagenesis

library(Biobase)

setwd(file.path("C:","Users","djenk","OneDrive","grad_school","05-2015_fall",
                "BS830_microarray","20151218-Final_Project"))

#TG-GATEs Data (Discovery Set)
load("Rat.Liver.in_vivo.repeat.annotated.RData")
tg.gates <- eSet

#Drug Matrix (Validation Set)
load("DM_liver_only.RData")
drug.matrix <- data_curated
rm(data_curated,eSet)

Here are the drugs that are in drug.matrix and TG-GATEs

intersect(unique(pData(drug.matrix)[,c("CHEMICAL")]),unique(as.character(pData(tg.gates)[,c("Chemical")])))
##  [1] "acetaminophen"        "acetazolamide"        "allyl alcohol"       
##  [4] "amiodarone"           "aspirin"              "azathioprine"        
##  [7] "carbamazepine"        "carbon tetrachloride" "clofibrate"          
## [10] "clomipramine"         "diazepam"             "diclofenac"          
## [13] "doxorubicin"          "ethanol"              "ethinylestradiol"    
## [16] "fenofibrate"          "gemfibrozil"          "ibuprofen"           
## [19] "indomethacin"         "ketoconazole"         "lomustine"           
## [22] "meloxicam"            "methapyrilene"        "methimazole"         
## [25] "naproxen"             "phenobarbital"        "promethazine"        
## [28] "propylthiouracil"     "simvastatin"          "tamoxifen"           
## [31] "thioacetamide"        "valproic acid"

Here are three drugs that seem to have different GenTox and Bacterial Mutagenesis columns. Everything else lines up except for four compounds that are listed as "NA" in TG-GATEs GenTox and have a value in Bacterial.Mutagenesis

pData(drug.matrix)[,c("CHEMICAL","GenTox")][grepl("carbon tetrachloride",pData(drug.matrix)[,c("CHEMICAL")]),]
##                       CHEMICAL GenTox
## 96002.CEL carbon tetrachloride      0
## 95898.CEL carbon tetrachloride      0
## 96740.CEL carbon tetrachloride      0
## 95760.CEL carbon tetrachloride      0
## 97401.CEL carbon tetrachloride      0
## 95919.CEL carbon tetrachloride      0
## 95766.CEL carbon tetrachloride      0
## 95700.CEL carbon tetrachloride      0
## 95745.CEL carbon tetrachloride      0
## 95849.CEL carbon tetrachloride      0
## 98044.CEL carbon tetrachloride      0
## 97540.CEL carbon tetrachloride      0
## 96653.CEL carbon tetrachloride      0
## 96011.CEL carbon tetrachloride      0
## 95998.CEL carbon tetrachloride      0
## 97406.CEL carbon tetrachloride      0
## 97534.CEL carbon tetrachloride      0
## 95808.CEL carbon tetrachloride      0
## 97404.CEL carbon tetrachloride      0
## 95713.CEL carbon tetrachloride      0
## 95944.CEL carbon tetrachloride      0
## 96699.CEL carbon tetrachloride      0
## 96734.CEL carbon tetrachloride      0
## 95918.CEL carbon tetrachloride      0

pData(tg.gates)[,c("Chemical","Bacterial.Mutagenesis")][grepl("carbon tetrachloride",pData(tg.gates)[,c("Chemical")]),]
##                        Chemical Bacterial.Mutagenesis
## 3017670011 carbon tetrachloride                    NA
## 3017670012 carbon tetrachloride                    NA
## 3017670013 carbon tetrachloride                    NA
## 3017670014 carbon tetrachloride                     1
## 3017670015 carbon tetrachloride                     1
## 3017670016 carbon tetrachloride                     1
## 3017670017 carbon tetrachloride                     1
## 3017670018 carbon tetrachloride                     1
## 3017670019 carbon tetrachloride                     1
## 3017670020 carbon tetrachloride                     1
## 3017670021 carbon tetrachloride                     1
## 3017670022 carbon tetrachloride                     1
## 3017670023 carbon tetrachloride                    NA
## 3017670024 carbon tetrachloride                    NA
## 3017670025 carbon tetrachloride                    NA
## 3017670026 carbon tetrachloride                     1
## 3017670027 carbon tetrachloride                     1
## 3017670028 carbon tetrachloride                     1
## 3017670029 carbon tetrachloride                     1
## 3017670030 carbon tetrachloride                     1
## 3017671001 carbon tetrachloride                     1
## 3017671002 carbon tetrachloride                     1
## 3017671003 carbon tetrachloride                     1
## 3017671004 carbon tetrachloride                     1
## 3017671029 carbon tetrachloride                    NA
## 3017671030 carbon tetrachloride                    NA
## 3017672001 carbon tetrachloride                    NA
## 3017672002 carbon tetrachloride                     1
## 3017672003 carbon tetrachloride                     1
## 3017672004 carbon tetrachloride                     1
## 3017672005 carbon tetrachloride                     1
## 3017672006 carbon tetrachloride                     1
## 3017672007 carbon tetrachloride                     1
## 3017672008 carbon tetrachloride                     1
## 3017672009 carbon tetrachloride                     1
## 3017672010 carbon tetrachloride                     1
## 3017672011 carbon tetrachloride                    NA
## 3017672012 carbon tetrachloride                    NA
## 3017672013 carbon tetrachloride                    NA
## 3017672014 carbon tetrachloride                     1
## 3017672015 carbon tetrachloride                     1
## 3017672016 carbon tetrachloride                     1
## 3017672017 carbon tetrachloride                     1
## 3017672018 carbon tetrachloride                     1
## 3017672019 carbon tetrachloride                     1
## 3017672020 carbon tetrachloride                     1
## 3017672021 carbon tetrachloride                     1
## 3017672022 carbon tetrachloride                     1

pData(drug.matrix)[,c("CHEMICAL","GenTox")][grepl("indomethacin",pData(drug.matrix)[,c("CHEMICAL")]),]
##               CHEMICAL GenTox
## 95468.CEL indomethacin      0
## 95370.CEL indomethacin      0
## 95450.CEL indomethacin      0
## 95994.CEL indomethacin      0
## 96879.CEL indomethacin      0
## 95376.CEL indomethacin      0
## 95340.CEL indomethacin      0
## 95411.CEL indomethacin      0

pData(tg.gates)[,c("Chemical","Bacterial.Mutagenesis")][grepl("indomethacin",pData(tg.gates)[,c("Chemical")]),]
##                Chemical Bacterial.Mutagenesis
## 3017706025 indomethacin                    NA
## 3017706026 indomethacin                    NA
## 3017706027 indomethacin                    NA
## 3017706028 indomethacin                     1
## 3017706029 indomethacin                     1
## 3017706030 indomethacin                     1
## 3017707001 indomethacin                     1
## 3017707002 indomethacin                     1
## 3017707003 indomethacin                     1
## 3017707004 indomethacin                     1
## 3017707005 indomethacin                     1
## 3017707006 indomethacin                     1
## 3017707007 indomethacin                    NA
## 3017707008 indomethacin                    NA
## 3017707009 indomethacin                    NA
## 3017707010 indomethacin                     1
## 3017707011 indomethacin                     1
## 3017707012 indomethacin                     1
## 3017707013 indomethacin                     1
## 3017707014 indomethacin                     1
## 3017707015 indomethacin                     1
## 3017707016 indomethacin                     1
## 3017707017 indomethacin                     1
## 3017707018 indomethacin                     1
## 3017708013 indomethacin                    NA
## 3017708014 indomethacin                    NA
## 3017708015 indomethacin                    NA
## 3017708016 indomethacin                     1
## 3017708017 indomethacin                     1
## 3017708018 indomethacin                     1
## 3017708019 indomethacin                     1
## 3017708020 indomethacin                     1
## 3017708021 indomethacin                     1
## 3017708022 indomethacin                     1
## 3017708023 indomethacin                     1
## 3017708024 indomethacin                     1
## 3017708025 indomethacin                    NA
## 3017708026 indomethacin                    NA
## 3017708027 indomethacin                    NA
## 3017708028 indomethacin                     1
## 3017708029 indomethacin                     1
## 3017708030 indomethacin                     1
## 3017709001 indomethacin                     1
## 3017709002 indomethacin                     1
## 3017709003 indomethacin                     1

pData(drug.matrix)[,c("CHEMICAL","GenTox")][grepl("methapyrilene",pData(drug.matrix)[,c("CHEMICAL")]),]
##                CHEMICAL GenTox
## 96290.CEL methapyrilene      0
## 96293.CEL methapyrilene      0
## 96307.CEL methapyrilene      0

pData(tg.gates)[,c("Chemical","Bacterial.Mutagenesis")][grepl("methapyrilene",pData(tg.gates)[,c("Chemical")]),]
##                 Chemical Bacterial.Mutagenesis
## 3017647024 methapyrilene                    NA
## 3017647025 methapyrilene                    NA
## 3017647026 methapyrilene                    NA
## 3017647027 methapyrilene                     1
## 3017647028 methapyrilene                     1
## 3017647029 methapyrilene                     1
## 3017647030 methapyrilene                     1
## 3017648001 methapyrilene                     1
## 3017648002 methapyrilene                     1
## 3017648003 methapyrilene                     1
## 3017648004 methapyrilene                     1
## 3017648005 methapyrilene                     1
## 3017648006 methapyrilene                    NA
## 3017648007 methapyrilene                    NA
## 3017648008 methapyrilene                    NA
## 3017648009 methapyrilene                     1
## 3017648010 methapyrilene                     1
## 3017648011 methapyrilene                     1
## 3017648012 methapyrilene                     1
## 3017648013 methapyrilene                     1
## 3017648014 methapyrilene                     1
## 3017648015 methapyrilene                     1
## 3017648016 methapyrilene                     1
## 3017648017 methapyrilene                     1
## 3017650030 methapyrilene                    NA
## 3017651001 methapyrilene                    NA
## 3017651002 methapyrilene                    NA
## 3017651003 methapyrilene                     1
## 3017651004 methapyrilene                     1
## 3017651005 methapyrilene                     1
## 3017651006 methapyrilene                     1
## 3017651007 methapyrilene                     1
## 3017651008 methapyrilene                     1
## 3017651009 methapyrilene                     1
## 3017651010 methapyrilene                     1
## 3017651011 methapyrilene                     1
## 3017651012 methapyrilene                    NA
## 3017651013 methapyrilene                    NA
## 3017651014 methapyrilene                    NA
## 3017651015 methapyrilene                     1
## 3017651016 methapyrilene                     1
## 3017651017 methapyrilene                     1
## 3017651018 methapyrilene                     1
## 3017651019 methapyrilene                     1
## 3017651020 methapyrilene                     1
## 3017651021 methapyrilene                     1
## 3017651022 methapyrilene                     1
## 3017651023 methapyrilene                     1
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment