基因组特征功能出错“；transcriptsByOverlaps（）；在R

通过subseq（）函数和DNAString函数（来自biomaRt）从chromosome1检索到DNA序列，我的目标是找到该序列中所有可能的转录本

我想找到GRange对象“Txdb”（人类1号染色体的所有转录本）和我之前获得的DNA序列（我必须构建一个GRange对象，将起始和结束位置放入chr1）之间的重叠，并使用函数transcriptsByOverlaps（）

代码如下：

>library(GenomicFeatures)

#download the pre compiled txDb annotation for Homo Sapiens from Bioconductor 
>library(TxDb.Hsapiens.UCSC.hg19.knownGene)

>txdb <-TxDb.Hsapiens.UCSC.hg19.knownGene

#building of the grange object
>(gr <- GRanges(seqnames = Rle("chr1", 1), ranges = IRanges(start =119625311, end = 129625309)))


  GRanges object with 1 range and 0 metadata columns:
      seqnames                 ranges strand
         <Rle>              <IRanges>  <Rle>
  [1]     chr1 [119625311, 129625309]      *
  -------
  seqinfo: 1 sequence from an unspecified genome; no seqlengths

>transcriptsByOverlaps(txdb, gr)   #this function needs a TranscriptsDb object and a grange one

 Error in .Call2("NCList_find_overlaps_in_groups", start(q), end(q), q_space,  : 
 when 'type' is "any", at least one of 'maxgap' and 'minoverlap' must be set to its default value

---

嗨，LenMar很高兴能帮助你缓解疼痛。你为我工作的代码。我认为可能是1）R版本或2）冲突包，我看到您在命名空间中加载了其他包，例如BSgenome.Hsapiens.UCSC.hg19 bioMarT等。您介意启动另一个R会话并使用运行上面的代码吗？通常在运行示例时会产生错误，原因是您安装的软件包版本不一致。使用

BiocManager:：valid（）

检查您的安装，并按照它给出的建议更新/降级软件包。谢谢你们@MartinMorgan我忘了说我在使用RStudio服务器，而不是我电脑上下载的程序。@MartinMorgan你能添加你的答案以接受它是正确的吗？嗨，LenMar很高兴能帮助你解决这个问题。你为我工作的代码。我认为可能是1）R版本或2）冲突包，我看到您在命名空间中加载了其他包，例如BSgenome.Hsapiens.UCSC.hg19 bioMarT等。您介意启动另一个R会话并使用运行上面的代码吗？通常在运行示例时会产生错误，原因是您安装的软件包版本不一致。使用

BiocManager:：valid（）

检查您的安装，并按照它给出的建议更新/降级软件包。谢谢你们@MartinMorgan我忘了说我是在使用RStudio服务器在线工作，而不是在我的电脑上使用下载的程序。@MartinMorgan你能添加你的答案以便接受它是正确的吗？

> txdb <- loadDb(system.file("extdata", "hg19_knownGene_sample.sqlite",
+                            package="GenomicFeatures"))
> gr <- GRanges(seqnames = rep("chr1",2),
+               ranges = IRanges(start=c(500,10500), end=c(10000,30000)),
+               strand = strand(rep("-",2)))

> transcriptsByOverlaps(txdb, gr)

Error in .Call2("NCList_find_overlaps_in_groups", start(q), end(q), q_space,  : 
  when 'type' is "any", at least one of 'maxgap' and 'minoverlap' must be set to its default value

R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.3 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=it_IT.UTF-8       LC_NUMERIC=C               LC_TIME=it_IT.UTF-8       
 [4] LC_COLLATE=it_IT.UTF-8     LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=it_IT.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg19_1.4.0       BSgenome_1.46.0                        
 [3] rtracklayer_1.36.6                      Biostrings_2.46.0                      
 [5] XVector_0.16.0                          TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [7] GenomicFeatures_1.28.5                  AnnotationDbi_1.40.0                   
 [9] Biobase_2.36.2                          GenomicRanges_1.30.3                   
[11] GenomeInfoDb_1.14.0                     IRanges_2.12.0                         
[13] S4Vectors_0.16.0                        BiocGenerics_0.24.0                    
[15] biomaRt_2.34.2                         

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14               pillar_1.1.0               compiler_3.4.1            
 [4] zlibbioc_1.22.0            prettyunits_1.0.2          bitops_1.0-6              
 [7] tools_3.4.1                progress_1.2.2             zeallot_0.1.0             
[10] digest_0.6.14              bit_1.1-12                 lattice_0.20-35           
[13] RSQLite_2.0                memoise_1.1.0              tibble_1.4.1              
[16] pkgconfig_2.0.1            rlang_0.4.1                Matrix_1.2-12             
[19] DelayedArray_0.2.7         DBI_0.7                    rstudioapi_0.7            
[22] GenomeInfoDbData_0.99.0    stringr_1.2.0              httr_1.3.1                
[25] knitr_1.18                 vctrs_0.2.0                hms_0.5.2                 
[28] grid_3.4.1                 bit64_0.9-7                R6_2.2.2                  
[31] BiocParallel_1.10.1        XML_3.98-1.9               blob_1.1.0                
[34] magrittr_1.5               matrixStats_0.52.2         GenomicAlignments_1.12.2  
[37] Rsamtools_1.28.0           backports_1.1.2            SummarizedExperiment_1.6.5
[40] assertthat_0.2.0           stringi_1.1.6              RCurl_1.95-4.10           
[43] crayon_1.3.4