TFEAresults-methods: The methods for TFEAresults-class

In jianhong/ATACseqTFEA: Transcription Factor Enrichment Analysis for ATAC-seq

The methods for TFEAresults-class

Description

The assessment and replacement methods for TFEAresults-class

Usage

getEnrichmentScore(x)

getBindingSites(x, TF)

getMotifID(x)

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

## S4 method for signature 'TFEAresults'
x$name

## S4 replacement method for signature 'TFEAresults'
x$name <- value

## S4 method for signature 'TFEAresults,ANY,ANY'
x[[i, j, ..., exact = TRUE]]

## S4 replacement method for signature 'TFEAresults,ANY,ANY'
x[[i, j, ...]] <- value

## S4 method for signature 'TFEAresults'
getEnrichmentScore(x)

## S4 method for signature 'TFEAresults'
getBindingSites(x, TF)

## S4 method for signature 'TFEAresults'
getMotifID(x)

Arguments

x	TFEAresults object.
TF	Transcription factor
object	an object of TFEAresults
name	A literal character string or a name (possibly backtick quoted).
value	value to replace.
i, j	indices specifying elements to extract or replace.
...	Named or unnamed arguments to form a signature.
exact	see Extract

Value

The 'getEnrichmentScore' method will return the enrichment score matrix.

The 'getBindingSites' method will return a GRanges object indicates binding sites.

The method 'getMotifID' will return A list of positions of the binding sites for the motifs.

Examples

res <- readRDS(system.file("extdata", "res.rds", package="ATACseqTFEA"))
as(res, "data.frame")
res
head(res$resultsTable)
head(res[["resultsTable"]])
head(getEnrichmentScore(res))

jianhong/ATACseqTFEA documentation built on Feb. 9, 2024, 4:09 a.m.