Description Usage Arguments Value Author(s) See Also Examples
View source: R/Geneset.intersect.R
The function Geneset.intersect
puts per method the results of the
PathwaysIter
function together for each cluster and takes the intersection
over the iterations per cluster per method. This is to see if over the
different resamplings of the data, similar pathways were discovered.
1 2 |
PathwaysOutput |
The output of the |
Selection |
Logical. Indicates whether or not the output of the pathways function were concentrated on a specific selection of compounds. If this was the case, Selection should be put to TRUE. Otherwise, it should be put to FALSE. |
sign |
The significance level to be handled for cutting of the pathways. |
names |
Optional. Names of the methods. |
seperatetables |
Logical. If TRUE, a separate element is created per cluster. containing the pathways for each iteration. |
separatepvals |
Logical. If TRUE, the p-values of the each iteration of each pathway in the intersection is given. If FALSE, only the mean p-value is provided. |
The output is a list with an element per method. For each method, it is portrayed per cluster which pathways belong to the intersection over all iterations and their corresponding mean p-values.
Marijke Van Moerbeke
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ## Not run:
data(fingerprintMat)
data(targetMat)
data(geneMat)
data(GeneInfo)
data(ListGO)
MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="ward",gap=FALSE,maxK=55,StopRange=FALSE)
L=list(MCF7_F,MCF7_T)
MCF7_Paths_FandT=PathwaysIter(list(MCF7_F,MCF7_T),GeneExpr=geneMat,nrclusters=7,
method=c("limma", "MLP"),ENTREZID=GeneInfo[,1],geneSetSource = "GOBP",top=NULL,
topG=NULL,GENESET=ListGO,sign=0.05,niter=2,fusionsLog=TRUE,WeightClust=TRUE,
names=c("FP","TP"))
MCF7_Paths_intersection=Geneset.intersect(MCF7_Paths_FandT,0.05,names=c("FP",
"TP"),seperatetables=FALSE,separatepvals=FALSE)
str(MCF7_Paths_intersection)
## End(Not run)
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