enrich | R Documentation |
enrich
enrich(
x,
object,
ontology = "",
pvalue = 0.05,
padj = NULL,
organism = NULL,
keytype = "",
filename = NULL,
minSize = 2,
maxSize = 500,
keepRich = TRUE,
padj.method = "BH",
sep = ",",
...
)
x |
vector contains gene names or dataframe with DEGs information |
object |
annotation data |
pvalue |
cutoff pvalue |
padj |
cutoff p adjust value |
organism |
organism |
keytype |
keytype for input genes |
filename |
output filename |
minSize |
minimal number of genes included in significant terms |
maxSize |
maximum number of genes included in significant terms |
keepRich |
keep terms with rich factor value equal 1 or not (default: TRUE) |
padj.method |
pvalue adjust method(default:"BH") |
sep |
character string used to separate the genes when concatenating |
richResult
Kai Guo
## Not run:
library(bioAnno)
fromKEGG(species="ath")
athgo <- buildOwn(dbname="org.ath.eg.db",anntype="GO")
athgo <- as.data.frame(athgo)
athgo <- na.omit(athgo)
gene <- sample(unique(athgo$GeneID),1000)
res <- enrich(gene,athgo)
## End(Not run)
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