#' Convert genes between symbol types
#'
#' Takes an input of genes and converts from inputed type to desired type
#'
#' @param genes The genes to convert.
#' @param from Gene symbol type of the input
#' @param to Desired gene symbol type for the output
#' @param mirror Mirror to use if redirect from primary site required
#' @importFrom biomaRt useMart
#' @importFrom biomaRt getLDS
#'
#' @return Data frame of genes with original and corresponding converted symbols
#' @export
convert_genes <- function(genes, from, to, mirror = "http://useast.ensembl.org/"){
if (from == 'ENSMUSG'){
srcMart = biomaRt::useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = mirror)
sourceAtts = 'ensembl_gene_id'
}
if (from == 'ENSG'){
srcMart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = mirror)
sourceAtts = 'ensembl_gene_id'
}
if (from == 'MGI'){
srcMart = biomaRt::useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = mirror)
sourceAtts = 'mgi_symbol'
}
if (from == 'HGNC'){
srcMart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = mirror)
sourceAtts = 'hgnc_symbol'
}
if (to == 'MGI'){
tarMart = biomaRt::useMart("ensembl", dataset = "mmusculus_gene_ensembl", host = mirror)
tarAtts = 'mgi_symbol'
}
if (to == 'HGNC'){
tarMart = biomaRt::useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = mirror)
tarAtts = 'hgnc_symbol'
}
genesV2 = biomaRt::getLDS(attributes = sourceAtts, filters = sourceAtts,
values = genes, mart = srcMart,
attributesL = tarAtts, martL = tarMart,
uniqueRows = F)
return(genesV2)
}
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