R列表中的.attrs和重复条目

Question

我试图使用这个R脚本从NCBI获取一些信息：

require(rentrez)
require(magrittr)
rs = "rs16891982"
rss = c("rs16891982", "rs12203592", "rs1408799", "rs10756819", "rs35264875", "rs1393350", "rs12821256", "rs17128291", "rs1800407", "rs12913832", "rs1805008", "rs4911414")
# given a rs number, return chr, bp, allele and gene name
annotateGeneName = function(rs) {
    anno = rentrez::entrez_search(db = "snp", term = rs) %>%
           "[["("ids")                                   %>%
           rentrez::entrez_summary(db = "snp", id = .)
           if(length(anno) < 1) {
               warning(sprintf("%s not found in dbSNP!", rs))
               return(invisible(NULL))
           }
           # there might be multiple entries
           # if "snp_id" is not in the list, then
           # it means multiple SNPs have been return for this search
           # just take the first hit
           if(! "snp_id" %in% names(anno)) {
               anno = anno[[1]]
           }
    chrpos = anno[["chrpos"]]
    EA     = anno$allele_origin %>% gsub("\\(.*", "", .)
    fEA    = anno$global_maf %>% gsub("/.*", "", .) %>% gsub("^.*=", "", .)
    genes  = dplyr::first(anno$genes, default = NA)
    res = data.frame(snp = rs, chrpos = chrpos, EA = EA, fEA = fEA, genes = genes)
    res
}
annotateGeneNames = function(rss) {
    do.call(rbind, lapply(rss, annotateGeneName))
}
ids = rentrez::entrez_search(db = "snp", term = rs) %>% "[["("ids")
x = rentrez::entrez_fetch(db = "snp", id = ids[1], rettype="xml")
snp1xml = xmlParse(x)
snp1list = xmlToList(snp1xml)
print(snp1list)

打印结果时，可以看到以下内容：

...
$Rs$Sequence$.attrs
     exemplarSs ancestralAllele 
    "285153617"   "C,C,C,C,C,C" 


$Rs$Ss$.attrs
        ssId       handle      batchId     locSnpId  subSnpClass       orient 
  "23456916"   "PERLEGEN"      "12309" "afd3693051"        "snp"    "forward" 
      strand      molType      buildId  methodClass    validated 
    "bottom"    "genomic"        "123"  "hybridize" "by-cluster" 


$Rs$Ss$.attrs
                          ssId                         handle 
                    "28510204"              "MGC_GENOME_DIFF" 
                       batchId                       locSnpId 
                       "12314" "BC064405x37550355-C16403799G" 
                   subSnpClass                         orient 
                         "snp"                      "forward" 
                        strand                        molType 
                      "bottom"                         "cDNA" 
                       buildId                    methodClass 
                         "126"                     "computed" 


$Rs$Ss
$Rs$Ss$Sequence
$Rs$Ss$Sequence$Seq5
[1] "TTCCCTTTCATTTTCCAGAGAAACTTGATCAGGAACCCACTGATTCCAAGAGCAAAGTAATCAGTGAGGAAATGACACCTAGAATTCATGATGAAAAAAGGATGCTTTATATGGTCCTTTTTAAGGTGATAGTTTTTCCTGACGTCCATAGATTTATTAAGAATCTGGTATTTTAAACAGTAGGAAATACACATAGAAATATCAAATCCAAGTTGTGCTAGACCAGAAACTTTTAGAAGACATCCTTAGGAGAGAGAAAGACTTACAAGAATAAAGTGAGGAAAACACGGAGTTGATGCA"

$Rs$Ss$.attrs

$Rs$Ss$Sequence
$Rs$Ss$Sequence$Seq5
[1] "AAGACATCCTTAGGAGAGAGAAAGACTTACAAGAATAAAGTGAGGAAAACACGGAGTTGATGCA"

$Rs$Assembly$Component$MapLoc$FxnSet
      geneId       symbol      mrnaAcc      mrnaVer      protAcc      protVer 
     "51151"    "SLC45A2"  "NM_016180"          "4"  "NP_057264"          "3" 
    fxnClass readingFrame       allele      residue   aaPosition 
 "reference"          "3"          "C"          "F"        "373" 

$Rs$Assembly$Component$MapLoc$FxnSet
                geneId                 symbol                mrnaAcc 
               "51151"              "SLC45A2"            "NM_016180" 
               mrnaVer                protAcc                protVer 
                   "4"            "NP_057264"                    "3" 
              fxnClass           readingFrame                 allele 
            "missense"                    "3"                    "G" 
               residue             aaPosition                 soTerm 
                   "L"                  "373" "non_synonymous_codon" 

这个列表中有很多.attrs条目，它们经常是重复的。还有其他重复的条目，例如：

$Rs$Ss$Sequence$Seq5
$Rs$Assembly$Component$MapLoc$FxnSet

等。

.attrs是什么意思，我如何理解这些数据？我不知道你怎么能在一个列表中有两个同名条目。

Answer 1

在R中，attributes和attr是赋值或提取属性的函数，但据我所知，‘..attr’只是一个列表位置名。它的意思本质上是作者认为它应该是什么意思.在此之后，您的代码完成了对XML的解析并将其转换为R列表。这不是R定义的一部分，所以请阅读文档。

我现在看到，您被具有相同名称的列表项所困扰。这在R中是可能的，"[“和”[“将检索与名称匹配的树中的第一项。访问将需要是数字的，或由lapply或sapply介导的，这些函数遍历树的上层，以避免歧义。

> mylist=vector("list", length=2)
> mylist
[[1]]
NULL

[[2]]
NULL

> names(mylist) <- c("a","a")
> mylist
$a
NULL

$a
NULL

> mylist[['a']]
NULL
> mylist['a']
$a
NULL

> lapply( mylist , "[[", "a")
$a
NULL

$a
NULL

(我也没有看到在提取和处理数据的过程中使用了这两种函数定义。)