Eoutput-method: Methods defined for S4 class Eoutput

In hfang-bristol/dcGOR: Analysis of Ontologies and Protein Domain Annotations

Methods defined for S4 class Eoutput

Description

Methods defined for S4 class Eoutput.

Usage

## S4 method for signature 'Eoutput'
show(object)

## S4 method for signature 'Eoutput'
zscore(x)

## S4 method for signature 'Eoutput'
pvalue(x)

## S4 method for signature 'Eoutput'
adjp(x)

## S4 method for signature 'Eoutput'
view(
x,
top_num = 5,
sortBy = c("pvalue", "adjp", "zscore", "nAnno", "nOverlap", "none"),
decreasing = NULL,
details = T
)

## S4 method for signature 'Eoutput'
write(x, file = "Eoutput.txt", verbose = T)

Arguments

object	an object of S4 class Eoutput. Usually this is an output from dcEnrichment
x	an object of S4 class Eoutput. Usually this is an output from dcEnrichment
top_num	the maximum number (5, by default) of terms will be viewed. If NULL or NA, all terms will be viewed (this can be used for the subsequent saving)
sortBy	which statistics will be used for sorting and viewing terms. It can be "pvalue" for p value, "adjp" for adjusted p value, "zscore" for enrichment z-score, "nAnno" for the number in domains annotated by a term, "nOverlap" for the number in overlaps, and "none" for ordering simply according to ID of terms
decreasing	logical to indicate whether to sort in a decreasing order. If it is null, by default it will be true for "zscore", "nAnno" or "nOverlap"; otherwise false
details	logical to indicate whether the detailed information of terms is also viewed. By default, it sets to TRUE for the inclusion
file	a character specifying a file name written into. By default, it is 'Eoutput.txt'
verbose	logical to indicate whether the messages will be displayed in the screen. By default, it sets to true for display

Value

view(x) returns a data frame with following components:

• term_id: term ID

• nAnno: number in domains annotated by a term

• nGroup: number in domains from the input group

• nOverlap: number in overlaps

• zscore: enrichment z-score

• pvalue: p value

• adjp: adjusted p value

• term_name: term name

• term_namespace: term namespace; optional, it is only appended when "details" is true

• term_distance: term distance; optional, it is only appended when "details" is true

• members: members (represented as domain IDs) in overlaps; optional, it is only appended when "details" is true

write(x) also returns the same data frame as view(x), in addition to a specified local file.

See Also

Eoutput-class

hfang-bristol/dcGOR documentation built on July 16, 2022, 6:43 p.m.