Hi,
I've run into a problem with the select function in org.At.tair.db. I'm looping through a list of Arabidopsis TAIR gene IDs and retrieving annotation info. It works fine until I reach a certain point in my list [812] and then I get an error saying that the key is not valid. As far as I can tell there's nothing wrong with the gene ID. It is the same format as all the others and I looked it up in tair and got a result. I've put in my code below. I hope it's clear enough. The first section is not very relevant as I'm just matching P.patens gene names to Arabidopsis homologue IDs before retrieving the info from org.At.tair.db.
Anyone know why this is happening? Any help would be appreciated.
#problematic code
for (i in 1:gene_num_contrast1_sig){
match_ID_sig <- Arabidopsis_ID[Arabidopsis_ID$V1 %like% paste(Pp_ID_contrast1_sig[i], "V3", sep = ""), ]
At_match_sig <- as.character(match_ID_sig[1,2])
At_ID_contrast1_sig <- c(At_ID_contrast1_sig, strsplit(At_match_sig, "\\.")[[1]][1])
if (is.na(At_ID_contrast1_sig[i])){
ann_contrast1_sig<- c(ann_contrast1_sig, NA)
}else{
ann<- select(org.At.tair.db, keytype = "TAIR", keys = At_ID_contrast1_sig[i], columns = "GENENAME")
ann_contrast1_sig<- c(ann_contrast1_sig, ann[1,2])}
}
#runs as expected until I get this error code when i=812
#Error in .testForValidKeys(x, keys, keytype, fks) :
#None of the keys entered are valid keys for 'TAIR'. Please use the keys method to see a listing of valid arguments.
#The gene ID at this index is "AT4G04605"
> sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
[5] LC_TIME=English_United Kingdom.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggridges_0.5.3 ggnewscale_0.4.5 DOSE_3.16.0 ggplot2_3.3.3
[5] enrichplot_1.10.2 data.table_1.14.0 stringr_1.4.0 org.At.tair.db_3.12.0
[9] AnnotationDbi_1.52.0 IRanges_2.24.1 S4Vectors_0.28.1 Biobase_2.50.0
[13] BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] fgsea_1.16.0 colorspace_1.4-1 ellipsis_0.3.2
[4] qvalue_2.22.0 XVector_0.30.0 GenomicRanges_1.42.0
[7] rstudioapi_0.13 farver_2.1.0 graphlayouts_0.7.1
[10] ggrepel_0.9.1 bit64_4.0.5 fansi_0.4.2
[13] scatterpie_0.1.6 xml2_1.3.2 splines_4.0.2
[16] cachem_1.0.4 GOSemSim_2.16.1 geneplotter_1.68.0
[19] polyclip_1.10-0 Rsamtools_2.6.0 annotate_1.68.0
[22] GO.db_3.12.1 dbplyr_2.1.1 ggforce_0.3.3
[25] BiocManager_1.30.16 compiler_4.0.2 httr_1.4.2
[28] rvcheck_0.1.8 assertthat_0.2.1 Matrix_1.2-18
[31] fastmap_1.1.0 cli_2.5.0 tweenr_1.0.2
[34] prettyunits_1.1.1 tools_4.0.2 igraph_1.2.6
[37] gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.4
[40] reshape2_1.4.4 DO.db_2.9 dplyr_1.0.6
[43] rappdirs_0.3.3 fastmatch_1.1-0 Rcpp_1.0.6
[46] vctrs_0.3.8 Biostrings_2.58.0 rtracklayer_1.49.5
[49] ggraph_2.0.5 lifecycle_1.0.0 clusterProfiler_3.18.1
[52] XML_3.99-0.6 zlibbioc_1.36.0 MASS_7.3-51.6
[55] scales_1.1.1 tidygraph_1.2.0 hms_1.1.0
[58] MatrixGenerics_1.2.1 SummarizedExperiment_1.20.0 RColorBrewer_1.1-2
[61] curl_4.3.1 memoise_2.0.0 gridExtra_2.3
[64] downloader_0.4 biomaRt_2.46.3 stringi_1.5.3
[67] RSQLite_2.2.7 genefilter_1.72.1 GenomicFeatures_1.42.3
[70] BiocParallel_1.24.1 GenomeInfoDb_1.26.7 rlang_0.4.11
[73] pkgconfig_2.0.3 matrixStats_0.58.0 bitops_1.0-7
[76] lattice_0.20-41 purrr_0.3.4 GenomicAlignments_1.26.0
[79] cowplot_1.1.1 shadowtext_0.0.8 bit_4.0.4
[82] tidyselect_1.1.1 plyr_1.8.6 magrittr_2.0.1
[85] DESeq2_1.30.1 R6_2.5.0 generics_0.1.0
[88] DelayedArray_0.16.3 DBI_1.1.1 withr_2.4.2
[91] pillar_1.6.1 survival_3.1-12 RCurl_1.98-1.3
[94] tibble_3.1.1 crayon_1.4.1 utf8_1.2.1
[97] BiocFileCache_1.14.0 viridis_0.6.1 progress_1.2.2
[100] locfit_1.5-9.4 grid_4.0.2 blob_1.2.1
[103] digest_0.6.27 xtable_1.8-4 tidyr_1.1.3
[106] openssl_1.4.4 munsell_0.5.0 viridisLite_0.4.0
[109] askpass_1.1
I must have hit Enter too soon, so you should come to the support site to see my full answer.