PhosphoExperiment-operate: PhosphoExperiment object subset, combine methods

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

PhosphoExperiment object subset, combine methods

Description

These are methods for combining or subsetting for PhosphoExperiment object. This provides some convenience for users.

Usage

## S4 method for signature 'PhosphoExperiment,ANY,ANY,ANY'
x[i, j, drop = TRUE]

## S4 replacement method for signature 'PhosphoExperiment,ANY,ANY,ANY'
x[i, j, ...] <- value

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

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

Arguments

x	A PhosphoExperiment object
i	For [,PhosphoExperiment, [,PhosphoExperiment<-, i, j are subscripts that can act to subset the rows of x
j	For [,PhosphoExperiment, [,PhosphoExperiment<-, i, j are subscripts that can act to subset the columns of x
drop	A logical(1), ignored by these methods
...	In cbind or rbind, a PhosphoExperiment objects
value	An object of a class specified in the S4 method signature.
deparse.level	See ?base::cbind for a description of this argument.

Available methods

In the following code snippets, ppe1 and ppe2 is a PhosphoExperiment object with matching colData. ppe3 and ppe4 is a PhosphoExperiment object with matching rowData.

rbind(ppe1, ppe2):

Combine row-wise

cbind(ppe3, ppe4):

Combine column-wise

Author(s)

Taiyun Kim

See Also

method rbind, cbind from SummarizedExperiment object.

Examples

example(PhosphoExperiment, echo = FALSE)

n = ncol(phosData)
ppe1 = phosData[,seq(round(n/2))]
ppe2 = phosData[,-seq(round(n/2))]

ppe = cbind(ppe1, ppe2)
identical(ppe, phosData)

ppe[,seq(round(n/2))] = ppe1
identical(ppe, phosData)

p = nrow(phosData)
ppe1 = phosData[seq(round(p/2)),]
ppe2 = phosData[-seq(round(p/2)),]

ppe = rbind(ppe1, ppe2)
identical(ppe, phosData)

ppe[seq(round(p/2)),] = ppe1
identical(ppe, phosData)

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