enrich | R Documentation |
CTDdata
objectsThis methods performs a fisher test using the genes in two objects of
class CTDdata
. The object in 'x' is used as source while
the object on 'y' is used as universe. When object 'x' corresponds to
an object created with query_ctd_gene
, the used genes
are the found terms in CTDbase. In the other cases (chemicals and
disease CTDdata
), the genes from the 'gene interactions'
table are used. If universe
is missing, all genes in CTDbase
are used as universe.
enrich(x, y, universe, use = "curated", warnings = TRUE, ...)
x |
Object of class |
y |
Object of class |
universe |
Vector of strings corresponding to the genes to be used as universe. |
use |
(default: |
warnings |
(default: |
... |
NOT USED |
A list with class htest
. Check
fisher.test
for more information.
# Example in a tryCatch, since we are performing a connection to a server we might # get a refused connection due to a server rejection. Evaluate the recieved HTTP # message to understand if the server is not available or if your IP adress is temporarly restricted tryCatch({ data("gala") air <- query_ctd_chem( terms = "Air Pollutants" ) hgnc_universe <- readRDS(paste0(path.package("CTDquerier"),"/extdata/universe.RDS")) enrich(gala, air, hgnc_universe) }, error = function(w){NULL})
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