Nothing
hu.mouse <- function(host="useast.ensembl.org", verbose=0, mouseHomologFilter="with_mmusculus_homolog")
##mouseHomologFilter used to be ""with_homolog_mmus"" in older versions of biomaRt.
{
## Uses Biomart Ensembel to compute a table with human ensembl genes
##^ at the first column and their homologs at the second column.
result <- list()
##
attributes <- c("ensembl_gene_id", "mmusculus_homolog_ensembl_gene")
if (require(biomaRt)){
ensembl <- biomaRt::useMart(biomart="ENSEMBL_MART_ENSEMBL",
verbose=max(verbose-2, 0),
dataset="hsapiens_gene_ensembl", host=host)
homologs <- biomaRt::getBM(attributes=attributes, values=TRUE,
filters=mouseHomologFilter, uniqueRows=TRUE,
mart=ensembl, verbose=max(verbose-2, 0))
} else {
stop("biomaRt package is required by hu.mouse()!")
}
expected <- "ensembl_gene_id-mmusculus_homolog_ensembl_gene"
if(paste(colnames(homologs), collapse="-") != expected)
stop("Unexpected output from biomaRt::getBM !")
colnames(homologs) <- c("human", "mouse")
## Mouse to human:
ids <- unique(homologs[, "mouse"])
mouse2huMatrix <- homologs[match(ids, homologs[, "mouse"]), ]
mouse2hu <- mouse2huMatrix[, "human"]
names(mouse2hu) <- mouse2huMatrix[, "mouse"]
## Human to mouse:
ids <- unique(homologs[, "human"])
hu2mouseMatrix <- homologs[match(ids, homologs[, "human"]), ]
hu2mouse <- hu2mouseMatrix[, "mouse"]
names(hu2mouse) <- hu2mouseMatrix[, "human"]
multiHu <- nrow(homologs)-length(hu2mouse)
multiMouse <- nrow(homologs)-length(mouse2hu)
message.if(paste("The number of non-unique human-mouse genes=", multiHu),
verbose=verbose)
message.if(paste("The number of non-unique mouse-human genes=", multiMouse),
verbose=verbose)
warning("Some genes with multiple homologs are selected arbitrarily.")
##
result[["homologs"]] <- homologs
result[["hu2mouse"]] <- hu2mouse
result[["mouse2hu"]] <- mouse2hu
result[["multiMouse"]] <- multiMouse
result[["multiHu"]] <- multiHu
return(result)
}
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