PhosphoExperiment-class {PhosR} | R Documentation |
The PhosphoExperiment class
PhosphoExperiment( ..., UniprotID = c(), GeneSymbol = c(), Site = c(), Residue = c(), Sequence = c(), Localisation = c() )
... |
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. |
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)