PhosphoExperiment: The PhosphoExperiment class

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

The PhosphoExperiment class

Description

The PhosphoExperiment class

Usage

PhosphoExperiment(
  ...,
  UniprotID = c(),
  GeneSymbol = c(),
  Site = c(),
  Residue = c(),
  Sequence = c(),
  Localisation = c()
)

Arguments

...	Arguments parsed, identical to those used to create SummarizedExperiment.
UniprotID	A character vector of Uniprot ID
GeneSymbol	A character vector of gene symbol
Site	A numeric vector of phosphorylation site
Residue	A character vector of site residue
Sequence	A character vector of sequences
Localisation	A localisation score.

Examples

data(phospho_L6_ratio)
quant <- as.matrix(phospho.L6.ratio)
uniprot <- as.character(sapply(strsplit(rownames(quant),";"), 
    function(x) x[[2]]))
symbol <- as.character(sapply(strsplit(rownames(quant),";"), 
    function(x) x[[2]]))
site <- as.numeric(gsub("[STY]","",sapply(strsplit(rownames(quant),";"), 
    function(x) x[[3]])))
res <- as.character(gsub("[0-9]","",sapply(strsplit(rownames(quant),";"), 
    function(x) x[[3]])))
seq <- as.character(sapply(strsplit(rownames(quant),";"), 
    function(x) x[[4]]))
phosData <- PhosphoExperiment(assays = list(Quantification = quant), 
    UniprotID = uniprot, Site = site, GeneSymbol = symbol, Residue = res, 
    Sequence = seq)

PYangLab/PhosR documentation built on Nov. 1, 2024, 1:47 p.m.