PhIPData-methods {PhIPData} | R Documentation

## Accessing and Modifying Information in PhIPData objects

### Description

Methods to extract and modify `assay(s)`(including convenient functions for `counts`, `logfc`, and `prob`), `sampleInfo`, `peptideInfo`, and `metadata`.

### Usage

    ## S4 method for signature 'PhIPData'
    counts(object, ...)

    logfc(object, ...)

    ## S4 method for signature 'PhIPData'
    logfc(object, ...)

    prob(object, ...)

    ## S4 method for signature 'PhIPData'
    prob(object, ...)

    peptideInfo(object, ...)

    ## S4 method for signature 'PhIPData'
    peptideInfo(object, ...)

    sampleInfo(object, ...)

    ## S4 method for signature 'PhIPData'
    sampleInfo(object, ...)

    ## S4 replacement method for signature 'PhIPData,list'
    assays(x, withDimnames = TRUE, ...) <- value

    ## S4 replacement method for signature 'PhIPData,SimpleList'
    assays(x, withDimnames = TRUE, ...) <- value

    ## S4 replacement method for signature 'PhIPData,missing'
    assay(x, i, withDimnames = TRUE, ...) <- value

    ## S4 replacement method for signature 'PhIPData,numeric'
    assay(x, i, withDimnames = TRUE, ...) <- value

    ## S4 replacement method for signature 'PhIPData,character'
    assay(x, i, withDimnames = TRUE, ...) <- value

    ## S4 replacement method for signature 'PhIPData'
    counts(object, ...) <- value

    logfc(object, ...) <- value

    ## S4 replacement method for signature 'PhIPData'
    logfc(object, ...) <- value

    prob(object, ...) <- value

    ## S4 replacement method for signature 'PhIPData'
    prob(object, ...) <- value

    peptideInfo(object) <- value

    ## S4 replacement method for signature 'PhIPData'
    peptideInfo(object) <- value

    sampleInfo(object, ...) <- value

    ## S4 replacement method for signature 'PhIPData'
    sampleInfo(object) <- value

### Arguments

`object` | A `PhIPData` object
`...` | parameters for `assays`, which are typically not needed.
`x` | A `PhIPData` object
`withDimnames` | Parameter for RangedSummarizedExperiment class functions. Overrided since row/column names are automatically synced within each object.
`value` | A `matrix`, `data.frame`, or DataFrame of the same dimensions (not necessarily the same names)
`i` | A `numeric`, character

### Details

In addition to the functions detailed in RangedSummarizedExperiment, the `PhIPData` class includes conveniently named functions to quickly access and modify frequently used components of PhIPData objects.

Replacement functions ensure that names of the replacement object are matched with the names of the `PhIPData` object.

Since packages for identifying differential expression in RNA-seq experiments are frequently used for estimating fold-changes for peptide enrichments, the class also includes coercion methods to and from DGELists.

### Value

Accessors: a DataFrame object

Setters: a `PhIPData` object

### Available methods

In the following code snippets, `x` is a PhIPData object, `value` is a matrix-like object with the same dimensions as `x`, and `...` are further arguments passed to `assay` (for the getter) or `assay<-` (for the setter).

`counts(x, ...)`, `counts(x, ...) <- value`:

  Get or set a matrix of raw read counts

`logfc(x, ...)`, `logfc(x, ...) <- value`:

  Get or set a matrix of log2 estimated fold changes (in comparison to beads-only samples)

`prob(x, ...)`, `pob(x, ...) <- value`:

  Get or set a matrix of probabilities associated with whether a sample has an enriched antibody response for a peptide.

### See Also

`assays` for SummarizedExperiment operations.

### Examples

    example("PhIPData")

    replacement_dat <- matrix(1L, nrow = 5, ncol = 5)

    ## SummarizedExperiment Accessors and Setters
    assays(phip_obj)
    assays(phip_obj)$counts <- replacement_dat
    assay(phip_obj, "logfc")
    assay(phip_obj, "logfc") <- replacement_dat

    ## counts
    counts(phip_obj)
    counts(phip_obj) <- counts_dat

    ## logfc
    logfc(phip_obj)
    logfc(phip_obj) <- logfc_dat

    ## prob
    prob(phip_obj)
    prob(phip_obj) <- replacement_dat

    ## coercion functions
    as(phip_obj, "DGEList")
    as(phip_obj, "List")
    as(phip_obj, "list")

[Package PhIPData version 1.0.0 Index]