enrichment {cogena} | R Documentation |
get the enrichment table from a cogena object with certain clustering methods and number of clusters.
enrichment( object, method, nCluster, CutoffNumGeneset = Inf, CutoffPVal = 0.05, orderMethod = "max", roundvalue = TRUE, add2 = FALSE ) ## S4 method for signature 'cogena' enrichment( object, method, nCluster, CutoffNumGeneset = Inf, CutoffPVal = 0.05, orderMethod = "max", roundvalue = TRUE, add2 = TRUE )
object |
a genecl or cogena object |
method |
as clMethods in genecl function |
nCluster |
as nClust in cogena function. |
CutoffNumGeneset |
the cut-off of the number of gene sets in the return table |
CutoffPVal |
the cut-off of p-value. The default is 0.05. |
orderMethod |
the order method, default is max, other options are "mean", "all", "I", "II" or a number meaning the ith cluster. |
roundvalue |
The default is TRUE. whether or not round the data. such as round(1.54, 1)=1.5 |
add2 |
enrichment score for add Up and Down reuglated genes. |
orderMethod:
max. ordered by the max value in clusters beside all
mean. ordered by the mean value in clusters beside all
All. ordered by all genes
I. ordered by the I cluster in two clusters (Up or Down-regulated, add2 should be TRUE)
II. ordered by the II cluster in two clusters (Up or Down-regulated, add2 should be TRUE)
a character number. like "3".
a matrix with clusters in row and gene-sets in column.
data(Psoriasis) annofile <- system.file("extdata", "c2.cp.kegg.v7.01.symbols.gmt.xz", package="cogena") ## Not run: genecl_result <- coExp(DEexprs, nClust=2:3, clMethods=c("hierarchical","kmeans"), metric="correlation", method="complete", ncore=2, verbose=TRUE) clen_res <- clEnrich(genecl_result, annofile=annofile, sampleLabel=sampleLabel) enrichment.table1 <- enrichment(clen_res, "kmeans", "3") enrichment.table2 <- enrichment(clen_res, "kmeans", "3", CutoffNumGeneset=10, orderMethod="mean") ## End(Not run)