dEnricherView {dnet} | R Documentation |
dEnricherView
is supposed to view results of enrichment analysis
by dEnricher
.
dEnricherView( eTerm, top_num = 10, sortBy = c("adjp", "pvalue", "zscore", "nAnno", "nOverlap", "none"), decreasing = NULL, details = F )
eTerm |
an object of class "eTerm" |
top_num |
the maximum number of gene sets (terms) will be viewed |
sortBy |
which statistics will be used for sorting and viewing gene sets (terms). It can be "adjp" for adjusted p value, "pvalue" for p value, "zscore" for enrichment z-score, "nAnno" for the number of sets (terms), "nOverlap" for the number in overlaps, and "none" for ordering according to ID of gene sets (terms) |
decreasing |
logical to indicate whether to sort in a decreasing order. If it is null, it would be true for "zscore", "nAnno" or "nOverlap"; otherwise it would be false |
details |
logical to indicate whether the detailed information of gene sets (terms) is also viewed. By default, it sets to false for no inclusion |
a data frame with following components:
setID
: term ID; as rownames
name
: term name
nAnno
: number in gene members annotated by a term
nOverlap
: number in overlaps
zscore
: enrichment z-score
pvalue
: nominal p value
adjp
: adjusted p value
namespace
: term namespace; optional, it is only appended
when "details" is true
distance
: term distance; optional, it is only appended
when "details" is true
members
: members (represented as Gene Symbols) in
overlaps; optional, it is only appended when "details" is true
none
#dEnricherView(eTerm, top_num=10, sortBy="adjp", decreasing=FALSE, details=TRUE)