kegH.RdKEGG human pathway GPS data, extracted by makeGPS, default settings.
This data can be used by sigora to preform signature
overrepresenation.
<http://www.genome.jp/kegg/pathway.html>
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., & Tanabe, M. 2012. “KEGG for integration and interpretation of large-scale molecular data sets.” Nucleic Acids Research 40(D1).
data(kegH) str(kegH) #> List of 6 #> $ origRepo :List of 3 #> ..$ : chr [1:305] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ... #> ..$ : chr [1:7453] "10327" "124" "125" "126" ... #> ..$ : int [1:26509, 1:2] 1 1 1 1 1 1 1 1 1 1 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "pwys" "gns" #> $ L1 :List of 6 #> ..$ GPS : int [1:973297, 1:3] 1 1 1 1 1 1 1 2 3 4 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:3] "rownames" "rownames" "S" #> ..$ PUG : int [1:3660, 1:2] 30 79 98 103 116 117 141 147 155 167 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "PU" "" #> ..$ gs : chr [1:7453] "10327" "124" "125" "126" ... #> ..$ ps : chr [1:305] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ... #> ..$ degs : 'table' int [1:7453(1d)] 2 2 2 78 2 1 1 1 3 1 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:7453] "10" "100" "1000" "10000" ... #> ..$ pwyszs: 'table' int [1:305(1d)] 68 30 30 34 33 31 27 18 27 44 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:305] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ... #> $ L2 :List of 6 #> ..$ GPS : int [1:1244, 1:3] 1 1 2 1 2 3 1 2 3 4 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:3] "rownames" "rownames" "S" #> ..$ PUG : int [1:80, 1:2] 1 2 3 4 5 6 7 8 9 10 ... #> .. ..- attr(*, "dimnames")=List of 2 #> .. .. ..$ : NULL #> .. .. ..$ : chr [1:2] "PU" "" #> ..$ gs : chr [1:80] "3155" "3157" "3158" "38" ... #> ..$ ps : chr [1:3] "hsa00072" "hsa04136" "hsa05330" #> ..$ degs : 'table' int [1:80(1d)] 1 1 1 1 1 1 1 1 1 1 ... #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:80] "102723407" "10533" "11337" "11345" ... #> ..$ pwyszs: 'table' int [1:3(1d)] 10 32 38 #> .. ..- attr(*, "dimnames")=List of 1 #> .. .. ..$ : chr [1:3] "hsa00072" "hsa04136" "hsa05330" #> $ repoName : chr "userrepo" #> $ pathwaydescriptions:'data.frame': 305 obs. of 2 variables: #> ..$ pwys: chr [1:305] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ... #> ..$ nms : chr [1:305] "Glycolysis / Gluconeogenesis" "Citrate cycle (TCA cycle)" "Pentose phosphate pathway" "Pentose and glucuronate interconversions" ... #> $ call : chr [1:3] "makeGPS" "mappingshsa_noznf" "hsaKEGG_GPS19.noznf.rda"