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Hello everyone: I would like to add "ORF IDs to Chromosomal Location" to my data frame named genes in the DGEList-object. The organism is yeast, and I downloaded org.Sc.sgd.db..
> columns(org.Sc.sgd.db)
[1] "ALIAS" "COMMON" "DESCRIPTION" "ENSEMBL" "ENSEMBLPROT"
[6] "ENSEMBLTRANS" "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL"
[11] "GENENAME" "GO" "GOALL" "INTERPRO" "ONTOLOGY"
[16] "ONTOLOGYALL" "ORF" "PATH" "PFAM" "PMID"
[21] "REFSEQ" "SGD" "SMART" "UNIPROT"
It seems org.Sc.sgd.db did not have datas about chromosome. However, the INDEX file in "Ubuntu\home\User1\R\x86_64-pc-linux-gnu-library\4.2\org.Sc.sgd.db" was shown below :
org.Sc.sgd.db Bioconductor annotation data package
org.Sc.sgdALIAS Map Open Reading Frame (ORF) Identifiers to Alias Gene Names
org.Sc.sgdCHR Map ORF IDs to Chromosomes
org.Sc.sgdCHRLENGTHS A named vector for the length of each of thechromosomes
org.Sc.sgdCHRLOC ORF IDs to Chromosomal Location
org.Sc.sgdCOMMON2ORF Map Between Yeast Common Names and ORFmIdentifiers
org.Sc.sgdDESCRIPTION An annotation data file that maps Open ReadingmFrame (ORF) identifiers to textural descriptions of the corresponding genes
org.Sc.sgdENSEMBL Map Ensembl gene accession numbers with SGD Gene identifiers
org.Sc.sgdENSEMBLPROT Map Ensembl protein acession numbers with SGD Gene identifiers
org.Sc.sgdENSEMBLTRANS Map Ensembl transcript acession numbers with SGD Gene identifiers
org.Sc.sgdENTREZID Map Systematic ORF identifiers with Entrez Gene identifiers
org.Sc.sgdENZYME Map between ORF IDs and Enzyme Commission (EC) Numbers
org.Sc.sgdGENENAME Map between ORF IDs and Genes
org.Sc.sgdGO Map between ORF IDs and Gene Ontology (GO)
org.Sc.sgdGO2ALLORFS Map Between Gene Ontology (GO) Identifiers and all ORF Identifiers in the subtree
org.Sc.sgdINTERPRO Map Yeast Systematic Names to InterPro IDs
org.Sc.sgdMAPCOUNTS Number of mapped keys for the maps in package org.Sc.sgd.db
org.Sc.sgdORGANISM The Organism for org.Sc.sgd
org.Sc.sgdPATH Mappings between ORF identifiers and KEGG pathway identifiers
org.Sc.sgdPMID Map between ORF Identifiers and PubMed Identifiers
org.Sc.sgdREFSEQ Map between systematic ORF identifiers and RefSeq Identifiers
org.Sc.sgdREJECTORF Rejected Yeast Genes (ORF)
org.Sc.sgdSGD Map Systematic ORF identifiers with SGD accession numbers
org.Sc.sgdSMART Map Yeast ORF Identifiers to SMART IDs
org.Sc.sgdUNIPROT Map Uniprot accession numbers with Systematic ORF identifiers
org.Sc.sgd_dbconn Collect information about the package annotation DB
How can I get the CHR from this package? Thanks.
> library(org.Sc.sgd.db)
> sessionInfo( )
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 23.04
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0
[2] BSgenome_1.66.3
[3] rtracklayer_1.58.0
[4] Biostrings_2.66.0
[5] XVector_0.38.0
[6] GenomicRanges_1.50.2
[7] GenomeInfoDb_1.34.9
[8] org.Sc.sgd.db_3.16.0
[9] yeast.db0_3.16.0
[10] AnnotationDbi_1.60.2
[11] IRanges_2.32.0
[12] S4Vectors_0.36.2
[13] Biobase_2.58.0
[14] AnnotationHub_3.6.0
[15] BiocFileCache_2.6.1
[16] dbplyr_2.4.0
[17] BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] MatrixGenerics_1.10.0 httr_1.4.7
[3] bit64_4.0.5 shiny_1.8.0
[5] interactiveDisplayBase_1.36.0 BiocManager_1.30.22
[7] blob_1.2.4 GenomeInfoDbData_1.2.9
[9] Rsamtools_2.14.0 yaml_2.3.7
[11] BiocVersion_3.16.0 pillar_1.9.0
[13] RSQLite_2.3.3 lattice_0.22-5
[15] glue_1.6.2 digest_0.6.33
[17] promises_1.2.1 htmltools_0.5.7
[19] httpuv_1.6.12 Matrix_1.6-1.1
[21] XML_3.99-0.15 pkgconfig_2.0.3
[23] zlibbioc_1.44.0 purrr_1.0.2
[25] xtable_1.8-4 later_1.3.1
[27] BiocParallel_1.32.6 tibble_3.2.1
[29] KEGGREST_1.38.0 generics_0.1.3
[31] ellipsis_0.3.2 cachem_1.0.8
[33] SummarizedExperiment_1.28.0 cli_3.6.1
[35] magrittr_2.0.3 crayon_1.5.2
[37] mime_0.12 memoise_2.0.1
[39] fansi_1.0.5 tools_4.2.2
[41] BiocIO_1.8.0 lifecycle_1.0.4
[43] matrixStats_1.1.0 DelayedArray_0.24.0
[45] compiler_4.2.2 rlang_1.1.2
[47] grid_4.2.2 RCurl_1.98-1.13
[49] rjson_0.2.21 rappdirs_0.3.3
[51] bitops_1.0-7 restfulr_0.0.15
[53] codetools_0.2-19 DBI_1.1.3
[55] curl_5.1.0 R6_2.5.1
[57] GenomicAlignments_1.34.1 dplyr_1.1.4
[59] fastmap_1.1.1 bit_4.0.5
[61] utf8_1.2.4 filelock_1.0.2
[63] parallel_4.2.2 Rcpp_1.0.11
[65] vctrs_0.6.4 png_0.1-8
[67] tidyselect_1.2.0
