dnet (version 1.1.7)

dGSEAview: Function to view enrichment results in a sample-specific manner

Description

dGSEAview is supposed to view results of gene set enrichment analysis but for a specific sample.

Usage

dGSEAview(
eTerm,
which_sample = 1,
top_num = 10,
sortBy = c("adjp", "gadjp", "ES", "nES", "pvalue", "FWER", "FDR",
"qvalue", "none"),
decreasing = NULL,
details = F
)

Arguments

eTerm

an object of class "eTerm"

which_sample

which sample will be viewed

top_num

the maximum number of gene sets will be viewed

sortBy

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

decreasing

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

details

logical to indicate whether the detail information of gene sets is also viewed. By default, it sets to false for no inclusion

Value

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

See Also

dGSEA

Examples

# NOT RUN {
#dGSEAview(eTerm, which_sample=1, top_num=10, sortBy="adjp", decreasing=FALSE, details=TRUE)
# }