kegH: Pathway GPS data, extracted from KEGG repository (Human).

Description Usage Source References See Also Examples

Description

KEGG human pathway GPS data, extracted by makeGPS, default settings. This data can be used by sigora to preform signature overrepresenation.

Usage

1
data("kegH")

Source

<http://www.genome.jp/kegg/pathway.html>

References

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).

See Also

makeGPS, sigora , reaH

Examples

1
2

Example output

List of 6
 $ origRepo           :List of 3
  ..$ : chr [1:303] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ...
  ..$ : chr [1:7324] "10327" "124" "125" "126" ...
  ..$ : int [1:26127, 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 [1:948751, 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 [1:3637, 1:2] 30 79 98 103 116 117 141 147 155 167 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:2] "PU" ""
  ..$ gs    : chr [1:7324] "10327" "124" "125" "126" ...
  ..$ ps    : chr [1:303] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ...
  ..$ degs  : 'table' int [1:7324(1d)] 2 2 2 77 2 1 1 1 2 1 ...
  .. ..- attr(*, "dimnames")=List of 1
  .. .. ..$ : chr [1:7324] "10" "100" "1000" "10000" ...
  ..$ pwyszs: 'table' int [1:303(1d)] 68 30 30 34 33 31 27 13 30 44 ...
  .. ..- attr(*, "dimnames")=List of 1
  .. .. ..$ : chr [1:303] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ...
 $ L2                 :List of 6
  ..$ GPS   : int [1:1709, 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 [1:111, 1:2] 1 2 3 4 5 6 7 8 9 10 ...
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : NULL
  .. .. ..$ : chr [1:2] "PU" ""
  ..$ gs    : chr [1:111] "3155" "3157" "3158" "38" ...
  ..$ ps    : chr [1:4] "hsa00072" "hsa03020" "hsa04136" "hsa05330"
  ..$ degs  : 'table' int [1:111(1d)] 1 1 1 1 1 1 1 1 1 1 ...
  .. ..- attr(*, "dimnames")=List of 1
  .. .. ..$ : chr [1:111] "102723407" "10533" "10621" "10622" ...
  ..$ pwyszs: 'table' int [1:4(1d)] 10 31 32 38
  .. ..- attr(*, "dimnames")=List of 1
  .. .. ..$ : chr [1:4] "hsa00072" "hsa03020" "hsa04136" "hsa05330"
 $ repoName           : chr "kegH"
 $ pathwaydescriptions:'data.frame':	303 obs. of  2 variables:
  ..$ pwys: chr [1:303] "hsa00010" "hsa00020" "hsa00030" "hsa00040" ...
  ..$ nms : chr [1:303] "Glycolysis / Gluconeogenesis" "Citrate cycle (TCA cycle)" "Pentose phosphate pathway" "Pentose and glucuronate interconversions" ...
 $ call               : chr [1:4] "makeGPS" "mappings.hsa" "../kegH.rda" "kegH"

sigora documentation built on Aug. 24, 2019, 1:04 a.m.