‘NSBS’ for signature 'SortedByQueryHits'

两种原因，ChIPseeker会出现如下报错 ‘unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits" ’。

1. bed文件和注释文件的染色体编号不一致。
   这个原因比较常见，自行修改染色体编号即可解决。

2. gtf格式有误。

   原gtf文件格式如下：

   A01 EVM transcript 1913 2559 . - . transcript_id "T0001"; gene_id "G0001";
   A01 EVM CDS 1913 2134 . - 0 transcript_id "T0001";
   A01 EVM CDS 2255 2365 . - 0 transcript_id "T0001";
   A01 EVM CDS 2491 2559 . - 0 transcript_id "T0001";

这种gtf进行annotatePeak时出现如上报错：

library(ChIPseeker)
library(GenomicFeatures)
TxDb <- makeTxDbFromGFF("Genome.gene.gtf")
x = annotatePeak(ben.file,tssRegion = c(-2000,0),TxDb = TxDb)
> preparing features information...      2021-12-23 11:17:36 
> identifying nearest features...        2021-12-23 11:17:36 
> calculating distance from peak to TSS...   2021-12-23 11:17:36 
> assigning genomic annotation...        2021-12-23 11:17:36 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’

经测试，将gtf改为如下格式，可解决报错问题：

EVM transcript 1913 2559 . - . transcript_id "T0001"; gene_id "G0001";
A01 EVM CDS 1913 2134 . - 0 transcript_id "T0001"; gene_id "G0001";
A01 EVM CDS 2255 2365 . - 0 transcript_id "T0001"; gene_id "G0001";
A01 EVM CDS 2491 2559 . - 0 transcript_id "T0001"; gene_id "G0001";