xEnrichViewer | R Documentation |
xEnrichViewer
is supposed to view results of enrichment
analysis.
xEnrichViewer(
eTerm,
top_num = 10,
sortBy = c("adjp", "fdr", "pvalue", "zscore", "fc", "nAnno",
"nOverlap", "or", "none"),
decreasing = NULL,
details = FALSE
)
eTerm |
an object of class "eTerm" |
top_num |
the number of the top terms (sorted according to 'sortBy' below) will be viewed |
sortBy |
which statistics will be used for sorting and viewing gene sets (terms). It can be "adjp" or "fdr" for adjusted p value (FDR), "pvalue" for p value, "zscore" for enrichment z-score, "fc" for enrichment fold change, "nAnno" for the number of sets (terms), "nOverlap" for the number in overlaps, "or" for the odds ratio, and "none" for ordering according to ID of 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:
id
: term ID; as rownames
name
: term name
nAnno
: number in members annotated by a term
nOverlap
: number in overlaps
fc
: enrichment fold changes
zscore
: enrichment z-score
pvalue
: nominal p value
adjp
: adjusted p value (FDR)
or
: a vector containing odds ratio
CIl
: a vector containing lower bound confidence interval
for the odds ratio
CIu
: a vector containing upper bound confidence interval
for the odds ratio
distance
: term distance or other information; optional, it
is only appended when "details" is true
members_Overlap
: members (represented as Gene Symbols) in
overlaps; optional, it is only appended when "details" is true
members_Anno
: members (represented as Gene Symbols) in
annotations; optional, it is only appended when "details" is true
none
xEnrichViewer
RData.location <- "http://galahad.well.ox.ac.uk/bigdata"
## Not run:
xEnrichViewer(eTerm)
## End(Not run)