I used the TTD database to identify a list of proteins that I want to highlight in a KEGG pathway map.
From this database I can extract the UniprotKB AC/ID for each protein. For example for HDAC1, this would be HDAC1_HUMAN. On the Uniprot website (https://www.uniprot.org/uploadlists/) I can enter that and select From UniProtKB AC/ID to GeneID (Entrez Gene), which will give me 3605 for the HDAC1_HUMAN protein. I am trying to do exactly this in RStudio with a vector of UniProt IDs that I want to convert to Entrez IDs. However, I couldn't manage and therefore wanted to ask whether someone can help me with this? I installed the Uniprot.ws package but cannot get a hold of which function to use.
So what I want to achieve is the following:
c(HDAC1_HUMAN,RIR2_HUMAN,PK3CG_HUMAN,TOP1_HUMAN,TOP2A_HUMAN, TOP2B_HUMAN,S19A1_HUMAN, PCFT_HUMAN)
Some R function to convert this
c(3065, 6241, 5294, 7150, 7153, 7155, 6573, 113235)
This output vector would then be used in the following function to highlight the proteins in two KEGG pathway maps:
pv.out <- pathview(gene.data = 'Output vector', pathway.id = c('hsa05200','hsa04110'), species = "hsa", out.suffix = "gse16873", kegg.native = T)
Which function can I use to achieve this?
Thanks a lot for your help!
R version 4.1.1 (2021-08-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19044) Matrix products: default attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  stringr_1.4.0 readr_2.1.2 UniProt.ws_2.34.0 BiocGenerics_0.40.0  RCurl_1.98-1.6 RSQLite_2.2.10 pathview_1.34.0