PhIPData-methods: Accessing and Modifying Information in PhIPData objects

In athchen/PhIPData: Container for PhIP-Seq Experiments

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")

athchen/PhIPData documentation built on Feb. 10, 2022, 1:34 a.m.