Nothing
## a function that takes the mapping between genes and arbitrary
## pathways as input (a list), fetches the necessary InterPro domains from
## biomaRt and creates an 'ipDataSource' object
dataSource <- function(mapping, type="generic"){
if(is.null(names(mapping)))
stop("'mapping' must be named list of pathway mappings to genes\n")
pathways <- as.character(unique(unlist(mapping)))
genes <- as.character(names(mapping))
## get corresponding interpro domains from biomaRt
ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
tmp <- getBM(attributes=c("entrezgene", "interpro"), filters="entrezgene",
values=genes, mart = ensembl, bmHeader=FALSE)
gene2Domains <- split(tmp$interpro, tmp$entrezgene, drop=FALSE)
missing <- setdiff(genes, names(gene2Domains))
gene2Domains[missing] <- ""
domains <- unique(unlist(gene2Domains))
domains <- domains[!is.na(domains)]
tmp2 <- unlist(mapping, use.names = FALSE)
path2Genes <- split(rep(genes, listLen(mapping)), tmp2)
path2Domains <- lapply(path2Genes, function(x, gene2Domains) unique(unlist(gene2Domains[x])),
gene2Domains)
## the lengths of pathway, gene and domain vectors
dims <- c(pathway=length(pathways), gene=length(genes),
domain=length(domains))
## create an object of class 'ipDataSource'
return(new("ipDataSource", genes=genes, pathways=pathways,
domains=domains, gene2Domains=gene2Domains,
path2Domains=path2Domains, dims=dims, type=type))
}
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