AnnotationForge函数makeOrgPackage中的“重复行”错误

如何解决AnnotationForge函数makeOrgPackage中的“重复行”错误

我正在使用AnnotationForge包，特别是函数makeOrgPackage创建一个有机体包。我一直在关注这个插图：https://www.bioconductor.org/packages/release/bioc/vignettes/AnnotationForge/inst/doc/MakingNewOrganismPackages.html

当我调用函数时：

makeOrgPackage(gene_info=PA14Sym,chromosome=PA14Chr,go=PA14Go,version="0.1",maintainer="myname <[e-mail]>",author="myname <[e-mail]>",outputDir = ".",tax_id="208963",genus="Pseudomonas",species="aeruginosa",goTable="go")

我收到此错误：

Error in FUN(X[[i]],...) : data.frames in '...' cannot contain duplicated rows

“ ...”是指包含注释数据的数据帧集。我确保这些数据框的结构与小插图中的示例完全相同。在“ gene_info”和“ chromosome” dfs中，我删除了所有重复的行。

“ go” df在“ GID”（基因ID）列中具有重复的值，但是所有GO值都是唯一的，并且我检查了是否存在重复的行。例如：

    GID         GO          EVIDENCE
1   PA14_00010  GO:0005524  ISM
2   PA14_00010  GO:0006270  ISM
3   PA14_00010  GO:0006275  ISM
4   PA14_00010  GO:0043565  ISM
5   PA14_00010  GO:0003677  ISM
6   PA14_00010  GO:0003688  ISM
7   PA14_00020  GO:0003677  ISM
8   PA14_00020  GO:0006260  ISM

小插图提供的样本雀科数据也是如此；重复的GID，但唯一的GO号。令人沮丧的是，当我为小插图中的示例数据运行makeOrgPackage函数时，没有任何错误。我在这里想念什么？

完整脚本：

# Load in GO annotated PA14 file,downloaded from Psuedomonas.com
PA14file <- read.csv("../data/GO_annotations/GO_PA14.csv")
colnames(PA14file)
> colnames(PA14file)
[1] "LocusTag"                "GeneName"                "ProductDescription"     
 [4] "StrainName"              "Accession"               "GOTerm"                 
 [7] "Namespace"               "GOEvidenceCode"          "EvidenceOntologyECOCode"
[10] "EvidenceOntologyTerm"    "SimilarToBindsTo"        "PMID"                   
[13] "chrom" 

# PA14 only has 1 chromosome,so create a new column and populate it with 1s.
PA14file$chrom <- '1'

# Create gene_info df,remove duplicate rows
PA14Sym <- PA14file[,c("LocusTag","GeneName","ProductDescription")]
PA14Sym <- PA14Sym[PA14Sym[,"GeneName"]!="-",]
PA14Sym <- PA14Sym[PA14Sym[,"ProductDescription"]!="-",]
colnames(PA14Sym) <- c("GID","SYMBOL","GENENAME")
PA14Sym <- PA14Sym[!duplicated(PA14Sym),]

# Create chromosome df,remove duplicate rows
PA14Chr <- PA14file[,"chrom")]
PA14Chr <- PA14Chr[PA14Chr[,"chrom"]!="-",]
colnames(PA14Chr) <- c("GID","CHROMOSOME")
PA14Chr %>% distinct(GID,.keep_all = TRUE)
PA14Chr <- PA14Chr[!duplicated(PA14Chr),]

# Create go df
PA14Go <- PA14file[,"Accession","GOEvidenceCode")]
PA14Go <- PA14Go[PA14Go[,"GOEvidenceCode"]!="",]
colnames(PA14Go) <- c("GID","GO","EVIDENCE")

# Call the function
makeOrgPackage(gene_info=PA14Sym,goTable="go")

解决方法

我今天也遇到了这个问题，刚刚在dplyr中改用distinct()后，这个函数就可以正常工作了。（我的和你的一样）

尝试在创建的每个部分的尾部添加一段 %>% dplyr::distinct() 或在所有操作后使用 dplyr::distinct() 删除变量中的重复项。

就你而言：

library(dplyr)
PA14Sym <- dplyr::distinct(PA14Sym)
PA14Chr <- dplyr::distinct(PA14Chr)
PA14Go <- dplyr::distinct(PA14Go)

希望这些能帮到你。