PhosphoExperiment-class {PhosR} | R Documentation

## 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)

[Package PhosR version 1.2.0 Index]