ctg开头的染色体号和geneChr不一样

[Sherry520]

library(ChIPseeker)
require(GenomicFeatures)
GFF_PATH = 'f:/07-CAUS/01-Linux-service/Maize_reference/B73-Ensembl-V4-48/Zea_mays.B73_RefGen_v4.48.gff3.gz'
maizev4.db <- makeTxDbFromGFF(GFF_PATH,format = "gff3")
peak <- readPeakFile("WRKY67-peak.rmchr.bed")
peakAnno <- annotatePeak("WRKY67-peak.rmchr.bed",tssRegion = c(-3000, 3000),TxDb = maizev4.db)
peakAnno.df <- as.data.frame(peakAnno)
openxlsx::write.xlsx(peakAnno.df,"WRKY67-peak.xlsx")

peak注释的结果中，染色体是ctg开头的，在geneChr的编号成了数字

> sessionInfo()
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8  LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

time zone: Asia/Shanghai
tzcode source: internal

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

other attached packages:
 [1] dplyr_1.1.4                             TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 ggplot2_3.4.4                          
 [4] GenomicFeatures_1.54.4                  AnnotationDbi_1.64.1                    Biobase_2.62.0                         
 [7] GenomicRanges_1.54.1                    GenomeInfoDb_1.38.1                     IRanges_2.36.0                         
[10] S4Vectors_0.40.2                        BiocGenerics_0.48.1                     ChIPseeker_1.38.0                      
[13] BiocManager_1.30.22                    

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3          jsonlite_1.8.7              rstudioapi_0.15.0           magrittr_2.0.3             
  [5] farver_2.1.1                rmarkdown_2.25              fs_1.6.3                    BiocIO_1.12.0              
  [9] zlibbioc_1.48.0             vctrs_0.6.4                 memoise_2.0.1               Rsamtools_2.18.0           
 [13] RCurl_1.98-1.13             ggtree_3.10.0               htmltools_0.5.7             S4Arrays_1.2.0             
 [17] progress_1.2.2              plotrix_3.8-4               curl_5.1.0                  SparseArray_1.2.2          
 [21] gridGraphics_0.5-1          KernSmooth_2.23-22          plyr_1.8.9                  cachem_1.0.8               
 [25] GenomicAlignments_1.38.1    igraph_1.5.1                lifecycle_1.0.4             pkgconfig_2.0.3            
 [29] Matrix_1.6-4                R6_2.5.1                    fastmap_1.1.1               GenomeInfoDbData_1.2.11    
 [33] MatrixGenerics_1.14.0       digest_0.6.33               aplot_0.2.2                 enrichplot_1.22.0          
 [37] colorspace_2.1-0            patchwork_1.1.3             DESeq2_1.42.0               RSQLite_2.3.3              
 [41] labeling_0.4.3              filelock_1.0.2              fansi_1.0.5                 httr_1.4.7                 
 [45] polyclip_1.10-6             abind_1.4-5                 compiler_4.3.2              bit64_4.0.5                
 [49] withr_2.5.2                 BiocParallel_1.36.0         viridis_0.6.4               DBI_1.1.3                  
 [53] gplots_3.1.3.1              ggforce_0.4.1               biomaRt_2.58.2              MASS_7.3-60                
 [57] rappdirs_0.3.3              DelayedArray_0.28.0         rjson_0.2.21                HDO.db_0.99.1              
 [61] caTools_1.18.2              gtools_3.9.5                tools_4.3.2                 scatterpie_0.2.1           
 [65] ape_5.7-1                   zip_2.3.0                   glue_1.6.2                  restfulr_0.0.15            
 [69] nlme_3.1-163                GOSemSim_2.28.0             shadowtext_0.1.2            grid_4.3.2                 
 [73] reshape2_1.4.4              fgsea_1.28.0                generics_0.1.3              gtable_0.3.4               
 [77] tidyr_1.3.0                 data.table_1.14.8           hms_1.1.3                   tidygraph_1.2.3            
 [81] xml2_1.3.5                  utf8_1.2.4                  XVector_0.42.0              ggrepel_0.9.4              
 [85] pillar_1.9.0                stringr_1.5.1               yulab.utils_0.1.0           splines_4.3.2              
 [89] tweenr_2.0.2                treeio_1.26.0               BiocFileCache_2.10.1        lattice_0.21-9             
 [93] rtracklayer_1.62.0          bit_4.0.5                   tidyselect_1.2.0            locfit_1.5-9.8             
 [97] GO.db_3.18.0                Biostrings_2.70.1           knitr_1.45                  gridExtra_2.3              
[101] SummarizedExperiment_1.32.0 xfun_0.41                   graphlayouts_1.0.2          factoextra_1.0.7           
[105] matrixStats_1.1.0           stringi_1.8.1               lazyeval_0.2.2              ggfun_0.1.3                
[109] yaml_2.3.7                  boot_1.3-28.1               evaluate_0.23               codetools_0.2-19           
[113] RMariaDB_1.3.1              ggraph_2.1.0                qvalue_2.34.0               tibble_3.2.1               
[117] ggplotify_0.1.2             cli_3.6.1                   munsell_0.5.0               Rcpp_1.0.11                
[121] dbplyr_2.4.0                png_0.1-8                   XML_3.99-0.16               parallel_4.3.2             
[125] blob_1.2.4                  prettyunits_1.2.0           DOSE_3.28.1                 bitops_1.0-7               
[129] tidytree_0.4.5              viridisLite_0.4.2           scales_1.2.1                openxlsx_4.2.5.2           
[133] purrr_1.0.2                 crayon_1.5.2                rlang_1.1.2                 cowplot_1.1.1              
[137] fastmatch_1.1-4             KEGGREST_1.42.0