dGSEAview
is supposed to view results of gene set enrichment
analysis but for a specific sample.
dGSEAview(
eTerm,
which_sample = 1,
top_num = 10,
sortBy = c("adjp", "gadjp", "ES", "nES", "pvalue", "FWER", "FDR",
"qvalue", "none"),
decreasing = NULL,
details = F
)
an object of class "eTerm"
which sample will be viewed
the maximum number of gene sets will be viewed
which statistics will be used for sorting and viewing gene sets. It can be "adjp" for adjusted p value, "gadjp" for globally adjusted p value, "ES" for enrichment score, "nES" for normalised enrichment score, "pvalue" for p value, "FWER" for family-wise error rate, "FDR" for false discovery rate, "qvalue" for q value, "none" for sorting by setID
logical to indicate whether to sort in a decreasing order. If it is null, it would be true for "ES" or "nES"; otherwise it would be false
logical to indicate whether the detail information of gene sets is also viewed. By default, it sets to false for no inclusion
a data frame with following components:
setID
: term ID
ES
: enrichment score
nES
: normalised enrichment score
pvalue
: nominal p value
adjp
: adjusted p value
gadjp
: globally adjusted p value
FDR
: false discovery rate
qvalue
: q value
setSize
: the number of genes in the set; optional, it is
only appended when "details" is true
name
: term name; optional, it is only appended when
"details" is true
namespace
: term namespace; optional, it is only appended
when "details" is true
distance
: term distance; optional, it is only appended
when "details" is true
# NOT RUN {
#dGSEAview(eTerm, which_sample=1, top_num=10, sortBy="adjp", decreasing=FALSE, details=TRUE)
# }
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