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我正在尝试使用 bioconductor 的 getBM() 函数来检索某些基因的序列。这是我的脚本：

setwd(".")
options(stringsAsFactors = FALSE)
cat("\014")


if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
listOfBiocPackages <- c("annotate", "GEOquery", "biomaRt")

bioCpackagesNotInstalled <- which( !listOfBiocPackages %in% rownames(installed.packages()) )
cat("package missing listOfBiocPackages[", bioCpackagesNotInstalled, "]: ", listOfBiocPackages[bioCpackagesNotInstalled], "\n", sep="")

# check there's still something left to install
if( length(bioCpackagesNotInstalled) ) {
    BiocManager::install(listOfBiocPackages[bioCpackagesNotInstalled])
}

library("easypackages")
libraries(listOfBiocPackages)  

mart <- useMart("ENSEMBL_MART_ENSEMBL")
mart <- useDataset("hsapiens_gene_ensembl", mart)

thisAnnotLookup <- getBM(mart=mart, attributes=c("affy_hg_u133a", "ensembl_gene_id", "gene_biotype", "external_gene_name", "gene_flank"), filter=c("affy_hg_u133a", "upstream_flank"), values=list(affyid=c("203423_at",   "204088_at",   "204511_at",   "204911_s_at", "205234_at")), uniqueRows=TRUE, checkFilters=FALSE)

print(thisAnnotLookup)

这个脚本给了我以下错误：

  'names' attribute [2] must be the same length as the vector [1]

我无法理解。

谁能帮我解决这个问题？谢谢！

4

1 回答 1

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如果您有两个过滤器，则需要提供 2 个元素的列表。然而，更大的问题是可能无法使用 upstream_flank ，具体取决于您的连接，请参阅此问题出现在许多用户中。对我来说，我上次使用了 asia mirror 并且它有效：

library(biomaRt)

mart <- useEnsembl(biomart = "ensembl", 
                   dataset = "hsapiens_gene_ensembl", 
                   mirror = "asia")

然后：

S = getSequence(id=c("203423_at","204088_at","204511_at","204911_s_at","205234_at"),
type="affy_hg_u133a",seqType="gene_flank",upstream = 20,mart = mart)

thisAnnotLookup <- getBM(mart=mart, 
attributes=c("affy_hg_u133a", "ensembl_gene_id", "gene_biotype", "external_gene_name"), 
filter="affy_hg_u133a", 
values=c("203423_at","204088_at","204511_at","204911_s_at","205234_at"), 
uniqueRows=TRUE, checkFilters=FALSE)

merge(thisAnnotLookup,S)
  affy_hg_u133a ensembl_gene_id   gene_biotype external_gene_name
1     203423_at ENSG00000114115 protein_coding               RBP1
2     204088_at ENSG00000135124 protein_coding              P2RX4
3     204511_at ENSG00000006607 protein_coding              FARP2
4   204911_s_at ENSG00000110171 protein_coding              TRIM3
5     205234_at ENSG00000168679 protein_coding            SLC16A4
            gene_flank
1 CTCCTCTTCCTTTGTAGGGG
2 GATTCCTCTCACCTCGGCCT
3 CGCGGGGGCTGCCGGCGGGC
4 CACCTTTCTACCCCTTAACT
5 GCCTGAGATGACATCAAATC

对我来说似乎超级挑剔。我认为你最好直接从基因组中获取序列。

于 2020-06-04T22:10:20.467 回答