由于subseq（）函数和DNAString函数（来自biomaRt），从第1号染色体检索了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号染色体上的所有转录本）和我先前获得的DNA序列（我必须用起点和终点位置构建一个Grange对象）之间的重叠。 chr1），其功能为 transcriptsByOverlaps（）。

代码如下：

stocks_return <- diff(log(stocks))

我什至运行了我在transcriptsByOverlaps（）函数帮助下找到的示例，并且得到了相同的错误：

>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

有人可以帮忙吗？我阅读了帮助，但不明白如何解决此问题。 谢谢。

这是SessionInfo（）

> 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",: 
  when 'type' is "any",at least one of 'maxgap' and 'minoverlap' must be set to its default value