PhosphoExperiment-methods: PhosphoExperiment object accessors

In PYangLab/PhosR: A set of methods and tools for comprehensive analysis of phosphoproteomics data

PhosphoExperiment object accessors

Description

These are methods for getting for setting accessors of PhosphoExperiment object. This provides some convenience for users.

Usage

UniprotID(x, ...)

UniprotID(x) <- value

GeneSymbol(x, ...)

GeneSymbol(x) <- value

Site(x, ...)

Site(x) <- value

Residue(x, ...)

Residue(x) <- value

Sequence(x, ...)

Sequence(x) <- value

Localisation(x, ...)

Localisation(x) <- value

## S4 method for signature 'PhosphoExperiment'
UniprotID(x, withDimnames = TRUE)

## S4 method for signature 'PhosphoExperiment'
GeneSymbol(x, withDimnames = TRUE)

## S4 method for signature 'PhosphoExperiment'
Site(x, withDimnames = TRUE)

## S4 method for signature 'PhosphoExperiment'
Residue(x, withDimnames = TRUE)

## S4 method for signature 'PhosphoExperiment'
Sequence(x, withDimnames = TRUE)

## S4 method for signature 'PhosphoExperiment'
Localisation(x, withDimnames = TRUE)

## S4 replacement method for signature 'PhosphoExperiment'
UniprotID(x) <- value

## S4 replacement method for signature 'PhosphoExperiment'
GeneSymbol(x) <- value

## S4 replacement method for signature 'PhosphoExperiment'
Site(x) <- value

## S4 replacement method for signature 'PhosphoExperiment'
Residue(x) <- value

## S4 replacement method for signature 'PhosphoExperiment'
Sequence(x) <- value

## S4 replacement method for signature 'PhosphoExperiment'
Localisation(x) <- value

Arguments

x	A PhosphoExperiment object to be assigned to.
...	Ignored for accessors.
value	A vector of values to set to respective accessor. See section Available methods for more details.
withDimnames	A logical(1), indicating whether the names of the vector should be applied.

Available methods

In the following code snippets, ppe is a PhosphoExperiment object.

UniprotID(ppe), UniprotID(ppe) <- value:

Get or set a Uniprot ID, where value is a character vector

GeneSymbol(ppe), GeneSymbol(ppe) <- value:

Get or set a gene symbol , where value is a character vector

Site(ppe), Site(ppe) <- value:

Get or set a phosphorylation site, where value is a numeric vector

Residue(ppe), Residue(ppe) <- value:

Get or set a residue of phosphorylation site, where value is a character

Sequence(ppe), Sequence(ppe) <- value:

Get or set a sequence, where value is a character vector

Localisation(ppe), Localisation(ppe) <- localisation:

Get or set a localisation score, where localisation is a numeric vector

Author(s)

Taiyun Kim

Examples

example(PhosphoExperiment, echo = FALSE)

UniprotID(phosData) <- uniprot
head(UniprotID(phosData))

GeneSymbol(phosData) <- symbol
head(GeneSymbol(phosData))

Site(phosData) <- site
head(Site(phosData))

Residue(phosData) <- res
head(Residue(phosData))

Sequence(phosData) <- seq
head(Sequence(phosData))

Localisation(phosData) <- rnorm(nrow(phosData))
head(Localisation(phosData))

PYangLab/PhosR documentation built on Feb. 3, 2024, 3:29 a.m.