兩種原因，ChIPseeker會(huì)出現(xiàn)如下報(bào)錯(cuò) ‘unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits" ’。

1. bed文件和注釋文件的染色體編號(hào)不一致。
   這個(gè)原因比較常見(jiàn)，自行修改染色體編號(hào)即可解決。

2. gtf格式有誤。

   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";

這種gtf進(jìn)行annotatePeak時(shí)出現(xiàn)如上報(bào)錯(cuò)：

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"’

經(jīng)測(cè)試，將gtf改為如下格式，可解決報(bào)錯(cuò)問(wèn)題：

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";