在R中与biomart循环播放

如何解决在R中与biomart循环播放

我有一个基于许多文件创建的数据集列表。

list.function <-  function() { 
   
  sample1 <- data.frame(ensembl.id = c("ENSG00000000005.6","ENSG00000000003.15","ENSG00000000419.13","ENSG00000000457.14","ENSG00000000460.17"),counts = c(4,5,6,1,1))
  sample2 <- data.frame(ensembl.id =  c("ENSG00000000005.6",1))
  sample3 <- data.frame(ensembl.id =  c("ENSG00000000005.6",1))
  sample4 <- data.frame(ensembl.id =  c("ENSG00000000005.6",1))
  
  sapply(paste('sample',seq(1,4,1),sep=''),get,environment(),simplify = FALSE) 
} 

my.list3 <- list.function()
my.list3



library("biomart")
grch38     <- useMart("ensembl",dataset="hsapiens_gene_ensembl")

我正在尝试自动执行此操作：

my.list4 = lapply(my.list3,function(x){
  
atributos = getBM(attributes = c("ensembl_gene_id_version","external_gene_name","chromosome_name","gene_biotype","entrezgene_description"),filters = "ensembl_gene_id_version",values = x$ensembl.id,mart = grch38)


atributos_unique = atributos %>% distinct(ensembl_gene_id_version,.keep_all = TRUE)


merged = merge(x,atributos_unique,by.x="ensembl.id",by.y="ensembl_gene_id_version" )


merged$gene_biotype = as.factor(merged$gene_biotype)
})

正确使用所有数据集的地方， 但无法正确输出！

我需要“合并的”最终输出对于我的“ my.list3”列表中的每个数据集都是唯一的，并且名称与原始数据集相同。

有什么想法吗？

解决方法

您不会在函数调用中返回数据帧。

library(biomaRt)
library(tidyverse)

grch38 = useMart("ensembl",dataset="hsapiens_gene_ensembl")

my.list4 = lapply(my.list3,function(x){
                  atributos = getBM(attributes = c("ensembl_gene_id_version","external_gene_name","chromosome_name","gene_biotype","entrezgene_description"),filters = "ensembl_gene_id_version",values = x$ensembl.id,mart = grch38)


               atributos_unique = atributos %>% 
                                     distinct(ensembl_gene_id_version,.keep_all = TRUE)


              merged = merge(x,atributos_unique,by.x="ensembl.id",by.y="ensembl_gene_id_version" )


              merged$gene_biotype = as.factor(merged$gene_biotype)
              return(merged) #or just merged
})

在函数调用的末尾添加return(merged)。