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

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

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

Note

none

See Also

dGSEA

Examples

#dGSEAview(eTerm, which_sample=1, top_num=10, sortBy="adjp", decreasing=FALSE, details=TRUE)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: supraHex
Loading required package: hexbin

dnet documentation built on Feb. 20, 2020, 3:01 p.m.