Description Usage Details Source Examples
A graph representing the apoptosis pathway from
KEGG, as well as a data.frame of attributes for use in plotting the
graph with Rgraphviz
and a list to compare the nodes with their
respective LocusLink IDs.
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The apopGraph
data set contains three objects:
The first is apopGraph
, which is an object of class
graph-NEL
and represents the hsa04210 graph from KEGG
.
The second is apopAttrs
, which is a data.frame with two columns,
and a row for every node in apopGraph
. The first column lists
what color the node is represented with on the KEGG
site. The
second column lists the type of the node - either genesym
or
text
. Most nodes are of type genesym
as they represent
genes, but some of the nodes in the KEGG
graph were not genes
and thus those nodes are of type text
.
The third, apopLocusLink
is a named list where the names
correspond to the node names in apopGraph
. The values of the
list are the LocusLink IDs that correspond to that node in the KEGG graph.
http://www.genome.ad.jp/kegg/pathway/hsa/hsa04210.html
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Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: Rgraphviz
Loading required package: grid
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