PPE-accessors {PhosR} | R Documentation

## 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))

[Package PhosR version 1.2.0 Index]