SilacProteinPeptideExperiment-accessors: Accessors for the SilacProteinExperiment and...

In pulsedSilac: Analysis of pulsed-SILAC quantitative proteomics data

Description

All the accessors, dimension, subsetting, merging and coercers that work on SilacProteinExperiment and SilacPeptideExperiment objects. Functions that work on SummarizedExperiment objects should also work on these two objects. Detailed examples of these functions can be found in the vignette of this package.

Usage

## S4 replacement method for signature 'SilacProteinExperiment,ANY'
assays(x) <- value

## S4 replacement method for signature 'SilacPeptideExperiment,ANY'
assays(x) <- value

## S4 method for signature 'SilacProteinExperiment'
cbind(..., deparse.level = 1)

## S4 method for signature 'SilacPeptideExperiment'
cbind(..., deparse.level = 1)

## S4 replacement method for signature 'SilacProteinExperiment,ANY'
colData(x, ...) <- value

## S4 replacement method for signature 'SilacPeptideExperiment,ANY'
colData(x, ...) <- value

## S4 method for signature 'SilacProteinExperiment'
metaoptions(x)

## S4 replacement method for signature 'SilacProteinExperiment'
metaoptions(x) <- value

## S4 method for signature 'SilacPeptideExperiment'
metaoptions(x)

## S4 replacement method for signature 'SilacPeptideExperiment'
metaoptions(x) <- value

## S4 method for signature 'SilacProteinExperiment'
rbind(..., deparse.level = 1)

## S4 method for signature 'SilacPeptideExperiment'
rbind(..., deparse.level = 1)

## S4 replacement method for signature 'SilacProteinExperiment'
rowData(x, ...) <- value

## S4 replacement method for signature 'SilacPeptideExperiment'
rowData(x, ...) <- value

## S4 method for signature 'SilacProteinExperiment'
subset(x, ...)

## S4 method for signature 'SilacPeptideExperiment'
subset(x, ...)

Arguments

x	A SilacProteinExperiment or a SilacPeptideExperiment object.
value	An object of class specified in the S4 method signature or as described in the following sections.
...	For rbind and cbind are SilacProteinExperiment or SilacPeptideExperiment objects to be joined together. For subset it is a logical comparison using a column name from the respective rowData data.frame. Otherwise unused.
deparse.level	Unused.

Value

Elements from SilacProteinExperiment or SilacPeptideExperiment objects.

Accessors

The following functions can be used to access the data in the class slots

assays:

Access the assays (list of matrices) of the object. Value should be a matrix or list of matrices.

assayNames

Access the assay names of the object. Value should be a character vector.

rowData

Access the protein/peptide feature data.frame of the object. Value should be data.frame with as many rows as proteins/peptides.

colData:

Access the samples data.frame of the object. Value should be a data.frame with as many rows as samples.

metadata:

Access the metadata list of the object. Value should be a list.

metaoptions:

Access the metaoptions list of the object. Value should be a list.

Dimensions

The following functions can be used to get the number of proteins/peptides and number of samples:

nrow:

Gives how many proteins and/or peptides the object has.

ncol:

Gives how many samples the object has.

dim:

Gives the number of proteins/peptides and the number of samples the object has.

length:

Gives how many proteins and/or peptides the object has.

Subsetting

The following functions can be used to subset the different classes:

$:

Gives a column from colData by name.

`[`:

Can be used to subset by row and column.

subset:

Allows to subset based on a logical comparison using a column name from the rowData data.frame.

Merging

The following functions can be used to aggregate objects of the same class together:

cbind:

Joins two or more objects horizontally (adding samples). Must have the same proteins/peptides and in the same order.

rbind:

Joins two or more objects vertically (adding proteins/peptides). Must have the same samples and in the same order.

merge:

Joins two objects by adding new samples and tries to merge the proteins/peptide rowData data.frames.

Merge methods are explained in detail in merge.

Coercers

The folloing functions can be used to transform a SilacProteinExperiment or a SilacPeptideExperiment into a SummarizedExperiment or a data.frame.

as(x, 'SummarizedEpriment'):

Transforms the object into an object of class SummarizedExperiment.

as(x, 'data.frame'):

Transforms the object into an object of class data.frame.

Examples

data('wormsPE')
protPE <- ProtExp(wormsPE)

# Accessors
## assays
assays(protPE)

## assaysNames
assayNames(protPE)

## colData
colData(protPE)

## rowData
rowData(protPE)

## metadata
metadata(protPE)

## metaoptions
#metaoptions(protPE)


# Dimensions
nrow(protPE)
ncol(protPE)
dim(protPE)
length(protPE)

# Subsetting
protPE$line
protPE[1,1]
subset(protPE, protein_id == 'AC3.2')

# Merging
rbind(protPE[1:10, ], protPE[11:20, ])
cbind(protPE[,1:2], protPE[,3:4])
#merge(protPE[1:10, 1:3], protPE[3:10, 4:5])

# Coercers
as(protPE, 'SummarizedExperiment')
as(protPE, 'data.frame')

pulsedSilac documentation built on Nov. 8, 2020, 5:13 p.m.