同源ID转换函数

https://zhuanlan.zhihu.com/p/141445523
https://blog.csdn.net/weixin_42655515/article/details/111167079
注意，要用亚洲的ensembl镜像，不然会很慢！host=http://asia.ensembl.org/

#-------------------------------------------------------
# Chapter:同源物种ID转换
#-------------------------------------------------------
get_id_conversion<-function(from,to,feature,attributes,filters,attributeL,host="http://asia.ensembl.org/"){
  require(biomaRt)
  # to="hsapiens_gene_ensembl"
  # from="mmusculus_gene_ensembl"
  # feature="Psme2b"
  # attributes="mgi_symbol"
  # filters="external_gene_name"
  # attributeL="hgnc_symbol"
  from_mart<-useMart("ENSEMBL_MART_ENSEMBL",dataset = from,host =host )
  to_mart<-useMart("ENSEMBL_MART_ENSEMBL",dataset = to,host = host)
  getLDS(attributes = attributes,
         filters = filters,
         values = feature,
         mart = from_mart,
         attributesL = attributeL,
         martL = to_mart)
  
}


get_id_conversion("mmusculus_gene_ensembl",
                  "hsapiens_gene_ensembl",
                  c("Pfkfb3","Akt2","Gpd2","Hmgcs2"),
                  "mgi_symbol",
                  "external_gene_name",
                  "hgnc_symbol")

常用的转换类型

ensembl_gene_id                             Gene stable ID
ensembl_gene_id_version                     Gene stable ID version
chromosome_name                   Chromosome/scaffold name
start_position                            Gene start (bp)
end_position                              Gene end (bp)
strand                                     Strand
band                             Karyotype band
external_gene_name                                    Gene name
gene_biotype                                    Gene type
hgnc_symbol                                                                  HGNC symbol
mgi_symbol                                  MGI symbol