equivClust {goProfiles} | R Documentation |
For a given level (2, 3, ...) in a GO ontology (BP, MF or CC), compute the equivalence threshold distance matrix and generate a dendrogram from it.
equivClust(ontoLevel, onto, geneLists, trace = TRUE, onTheFlyDev = NULL, method = "complete", jobName = paste("Equivalence cluster", onto, ontoLevel, method, sep = "_"), ylab = "Equivalence threshold distance", alpha = 0.05, precis = 0.001, ...)
ontoLevel |
integer (2, 3, ...) level of a GO ontology where the GO profiles are built |
onto |
character, GO ontology ("BP", "MF" or "CC") under consideration |
geneLists |
list of character vectors, each vector stands for the gene names in a given gene set |
trace |
boolean, the full process must be traced? Defaults to TRUE |
onTheFlyDev |
character, name of the graphical device where to immediately display the resulting
diagram. The appropriate names depend on the operating system. Defaults to |
method |
character, one of the admissible methods in function |
jobName |
character, main plot name, defaults to
|
ylab |
character, label of the vertical axis of the plot, defaults to "Equivalence threshold distance" |
alpha |
simultaneous nominal significance level for the equivalence tests to be repeteadly performed, defaults to 0.05 |
precis |
numerical precission in the iterative search of the equivalence threshold distances, defaults to 0.001 |
... |
additional arguments to |
Do not confuse the threshold distance matrix with the squared distances computed in each equivalence test.
An object of class equivClust
, descending from class hclust
with some additional attributes:
The main job name
The graphic subtittle
The vertical axis label
The equivalence threshold distance matrix
A list with some information on all the pairwise equivalence tests: the Euclidean squared distance, its standard error and the corresponding GO profiles
## Not run: data(kidneyGeneLists) clustMF2 <- equivClust(2, "MF", kidneyGeneLists, orgPackage="org.Hs.eg.db") plot(clustMF2) plot(clustMF2, main = "Dendrogram (method = complete)", sub = attr(clustMF2, "sub"), ylab = "Equivalence threshold distance") # With the same data, an UPGMA dendrogram: equivClust(2, "MF", kidneyGeneLists, method = "average", orgPackage="org.Hs.eg.db") ## End(Not run)