Description Usage Arguments Details Value See Also
Report GO/KEGG analysis.
1 2 | report_enrichment(all.cpg, sig = 0.05, collection = "GO", prefix = NULL,
invisible = T)
|
all.cpg |
named vector, with significance or any value to subset significant probes |
sig |
threshold used to subset the probes. Probes below or equal to the threshold are selected |
collection |
'GO' or 'KEGG' |
prefix |
file prefix to write the results. It must point to a valid folder |
invisible |
a boolean to determine if the output of 'missMethyl::gometh' is returned |
This function is a wrapper for the 'gometh' function from 'missMethyl' package that directly writes the results into a folder specified in 'prefix'.
A data frame with a row for each GO or KEGG term and the following columns:
Term |
GO term if testing GO pathways |
Ont |
ontology that the GO term belongs to if testing GO pathways. "BP" - biological process, "CC" - cellular component, "MF" - molecular function. |
Pathway |
the KEGG pathway being tested if testing KEGG terms. |
N |
number of genes in the GO or KEGG term |
DE |
number of genes that are differentially methylated |
P.DE |
p-value for over-representation of the GO or KEGG term term |
FDR |
False discovery rate |
missMethyl::gometh
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