reaM.RdReactome mouse pathway GPS data, extracted by makeGPS, default
settings. This data can be used by sigora to preform signature
overrepresenation.
<http://www.reactome.org/>
Matthews, L., Gopinath, G., Gillespie, M., Caudy, M., Croft, D., et al. 2009. “Reactome knowledgebase of human biological pathways and processes.” Nucleic acids research 37(Database issue).
data(reaM) str(reaM) #> List of 9 #> $ origRepo :List of 3 #> ..$ : Factor w/ 1630 levels "R-MMU-1059683",..: 96 1146 314 1380 1381 1469 1471 153 190 525 ... #> ..$ : int [1:8441] 100009614 100017 100034361 100037258 100038882 100038927 100039053 100039319 100039707 100039863 ... #> ..$ : int [1:52675, 1:2] 1 2 3 4 5 6 7 8 9 10 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "pwys" "gns" #> $ L1 :List of 6 #> ..$ GPS : int [1:759241, 1:3] 5 3 5 8 5 17 45 48 49 5 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:3] "rownames" "rownames" "S" #> ..$ PUG : int [1:641, 1:2] 60 62 93 95 100 117 137 144 151 154 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "PU" "" #> ..$ gs : chr [1:8441] "100009614" "100017" "100034361" "100037258" ... #> ..$ ps : chr [1:1025] "R-MMU-1266738" "R-MMU-6805567" "R-MMU-174824" "R-MMU-8856825" ... #> ..$ degs : 'table' int [1:8441(1d)] 2 5 3 2 8 3 5 46 3 5 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:8441] "100009614" "100017" "100034361" "100037258" ... #> ..$ pwyszs: 'table' int [1:1025(1d)] 104 38 40 11 34 25 14 61 64 21 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:1025] "R-MMU-109581" "R-MMU-109606" "R-MMU-109704" "R-MMU-110312" ... #> $ L2 :List of 6 #> ..$ GPS : int [1:472001, 1:3] 1 1 13 9 1 13 14 1 13 14 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:3] "rownames" "rownames" "S" #> ..$ PUG : int [1:2303, 1:2] 1 4 13 14 16 17 20 21 23 25 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "PU" "" #> ..$ gs : chr [1:7771] "100009614" "100017" "100034361" "100037258" ... #> ..$ ps : chr [1:895] "R-MMU-6805567" "R-MMU-8856825" "R-MMU-8964038" "R-MMU-8964043" ... #> ..$ degs : 'table' int [1:7771(1d)] 1 3 2 1 6 2 3 35 2 3 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:7771] "100009614" "100017" "100034361" "100037258" ... #> ..$ pwyszs: 'table' int [1:895(1d)] 104 38 40 11 34 25 14 61 64 21 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:895] "R-MMU-109581" "R-MMU-109606" "R-MMU-109704" "R-MMU-110312" ... #> $ L3 :List of 6 #> ..$ GPS : int [1:145645, 1:3] 4 18 4 11 4 11 21 4 11 21 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:3] "rownames" "rownames" "S" #> ..$ PUG : int [1:1946, 1:2] 1 2 4 7 18 20 21 22 23 24 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "PU" "" #> ..$ gs : chr [1:5212] "100017" "100034361" "100038882" "100038927" ... #> ..$ ps : chr [1:627] "R-MMU-8964038" "R-MMU-2129379" "R-MMU-110313" "R-MMU-1169408" ... #> ..$ degs : 'table' int [1:5212(1d)] 1 1 4 1 2 23 1 2 2 2 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:5212] "100017" "100034361" "100038882" "100038927" ... #> ..$ pwyszs: 'table' int [1:627(1d)] 38 40 11 34 25 14 61 64 21 10 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:627] "R-MMU-109606" "R-MMU-109704" "R-MMU-110312" "R-MMU-110313" ... #> $ L4 :List of 6 #> ..$ GPS : int [1:46736, 1:3] 2 2 4 2 4 5 7 7 2 4 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:3] "rownames" "rownames" "S" #> ..$ PUG : int [1:986, 1:2] 2 4 5 6 9 12 13 14 15 21 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "PU" "" #> ..$ gs : chr [1:2855] "100038882" "100039053" "100039319" "100039863" ... #> ..$ ps : chr [1:379] "R-MMU-1169408" "R-MMU-5656169" "R-MMU-380108" "R-MMU-110330" ... #> ..$ degs : 'table' int [1:2855(1d)] 2 1 14 1 1 1 3 23 1 2 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:2855] "100038882" "100039053" "100039319" "100039863" ... #> ..$ pwyszs: 'table' int [1:379(1d)] 40 11 14 61 64 21 10 12 36 15 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:379] "R-MMU-109704" "R-MMU-110312" "R-MMU-110320" "R-MMU-110330" ... #> $ L5 :List of 6 #> ..$ GPS : int [1:22129, 1:3] 5 12 12 21 5 12 26 27 2 44 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:3] "rownames" "rownames" "S" #> ..$ PUG : int [1:204, 1:2] 12 35 43 52 58 72 89 114 117 120 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "PU" "" #> ..$ gs : chr [1:1590] "100039319" "100041230" "100042807" "100043507" ... #> ..$ ps : chr [1:234] "R-MMU-110330" "R-MMU-110331" "R-MMU-171306" "R-MMU-5250913" ... #> ..$ degs : 'table' int [1:1590(1d)] 8 15 9 10 19 11 11 11 2 11 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:1590] "100039319" "100041230" "100042807" "100043507" ... #> ..$ pwyszs: 'table' int [1:234(1d)] 40 11 61 64 12 15 24 25 24 54 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:234] "R-MMU-109704" "R-MMU-110312" "R-MMU-110330" "R-MMU-110331" ... #> $ repoName : chr "reactomeMouseTASIEA" #> $ pathwaydescriptions:'data.frame': 1025 obs. of 2 variables: #> ..$ pwys: Factor w/ 1025 levels "R-MMU-109581",..: 52 740 181 896 897 945 946 83 108 321 ... #> ..$ nms : Factor w/ 1025 levels "A tetrasaccharide linker sequence is required for GAG synthesis",..: 210 458 656 104 153 466 657 274 245 528 ... #> $ call : chr [1:4] "makeGPS" "tmpdf" "reamdfGPS.rda" "reactomeMouseTASIEA"