R/listSNPFilters.r

In liuyufong/AnimalGene2QTL: Get the QTL/gene/SNP data functions

#' list of snp attributes and filters.
#'
#' @param data_set, choose one of '1,2,3,4,5'.'1' = 'btaurus_snp',2' = 'ggallus_snp','3' = 'ecaballus_snp',4' = 'sscrofa_snp','5' = 'oaries_s
#' @return result
#' @export
#' @importFrom biomaRt listMarts
#' @importFrom biomaRt useEnsembl
#' @importFrom biomaRt useMart
#' @importFrom biomaRt listFilters
#' @export
#' @examples
#' listSNPFilters(1)
listSNPFilters <- function(data_set) {
    for (pkg in c("biomaRt")) {
        if (!requireNamespace(pkg, quietly = TRUE)) {
            stop(paste("the ", pkg, " package needed for this function to work. Please install it.", 
                sep = ""), call. = FALSE)
        }
    }
    snpdataset <- switch(data_set, `1` = "btaurus_snp", `2` = "ggallus_snp", `3` = "ecaballus_snp", 
        `4` = "sscrofa_snp", `5` = "oaries_snp")
    if (data_set == 2) {
        ensembl <- useEnsembl("ensembl", version = 85)
        message("The version of chicken QTL is 4.0,and the version of SNP is 4.0!")
        host <- "grch37.ensembl.org"
    } else {
        ensembl <- useEnsembl("ensembl")
        host <- "www.ensembl.org"
    }
    martlist <- listMarts(ensembl)
    if (data_set == 2) {
        mart <- useMart(martlist[2, 1], dataset = snpdataset, host = host)
    } else {
        mart <- useMart(martlist[3, 1], dataset = snpdataset, host = host)
    }
    result <- listFilters(mart)
    return(result)
}