Question

我想转换一组基因，我可以用biomart转换它们

musGenes <- c("Hmmr", "Tlx3","STSRAAA1", "Cpeb4")
convertMouseGeneList <- function(x){
require("biomaRt")
human = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
genesV2 = getLDS(attributes = c("mgi_symbol"), filters = "mgi_symbol", values = x , mart = mouse, attributesL = c("hgnc_symbol"), martL = human, uniqueRows=T)
humanx <- unique(genesV2[, 2])
return(humanx)
}

它将仅返回数据库中的那些但不显示哪些不存在。在biomart中是否有一项功能是不让它与数据重叠？例如，在这种情况下，它应该为＆＃34; STSRAAA1＆＃34;

返回空

例如，所需的输出应该如下所示

Hmmr 
Tlx3
- 
Cpeb4

Answer 1

我认为最简单的解决方案是将鼠标基因符号存储在数据框（而不是矢量）中，其名称与getLDS()返回的列名相同。然后，您可以使用例如 merge()加入输出。

library(biomaRt)
human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
mouse <- useMart("ensembl", dataset = "mmusculus_gene_ensembl")

musGenes <- data.frame(MGI.symbol = c("Hmmr", "Tlx3","STSRAAA1", "Cpeb4"),
                       stringsAsFactors = FALSE)

genesV2 <- getLDS(attributes = c("mgi_symbol"), 
                  filters = "mgi_symbol", 
                  values = musGenes$MGI.symbol, 
                  mart = mouse, 
                  attributesL = c("hgnc_symbol"), 
                  martL = human)

merge(musGenes, genesV2, all = TRUE)

  MGI.symbol HGNC.symbol
1      Cpeb4       CPEB4
2       Hmmr        HMMR
3   STSRAAA1        <NA>
4       Tlx3        TLX3

我怎样才能找到哪些基因被转化而哪些基因不被转化

1 个答案: