upDownGene {cogena} | R Documentation |
The value means up or down regulated genes for each cluster. 1 suggests that genes in the cluster is up-regualted genes, while -1 down-regualted genes. value within (-1, 1) means genes there are both up and down regulated genes in the cluster. Return a vector with the length of nCluster if add2 is FALSE, or the length of nCluster + 2 if add2 is TRUE and nCluster is not 2. In the latter situation, the last two itemes represent Up and Down reuglated genes
upDownGene(object, method, nCluster, add2 = FALSE) ## S4 method for signature 'cogena' upDownGene(object, method, nCluster, add2 = FALSE) logfc(dat, sampleLabel)
object |
a genecl or cogena object |
method |
as clMethods in genecl function |
nCluster |
cluster number |
add2 |
add2 enrichment score for add Up and Down reuglated genes |
dat |
gene expression data frame |
sampleLabel |
factor. sampleLabel with names |
upDownGene: a vector
logfc: a data.frame
data(Psoriasis) annofile <- system.file("extdata", "c2.cp.kegg.v5.0.symbols.gmt.xz", package="cogena") 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) upDownGene(clen_res, "kmeans", "3", add2=TRUE) upDownGene(clen_res, "kmeans", "2", add2=FALSE)