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If I want to retrieve the identifier of a protein in Reactome using the ENTREZ id I can't, both the PATHID and the REACTOMEID are the same. While if I understood correctly they should be different, REACTOMEID, would be the identifier for such protein and PATHID the identifier of the pathway where such protein is involved.
>library("reactome.db")
> select(reactome.db, keys = "3855", keytype = "ENTREZID", columns = "REACTOMEID")
'select()' returned 1:many mapping between keys and columns
ENTREZID REACTOMEID
1 3855 R-HSA-1266738
2 3855 R-HSA-6805567
3 3855 R-HSA-6809371
> select(reactome.db, keys = "3855", keytype = "ENTREZID", columns = "PATHID")
'select()' returned 1:many mapping between keys and columns
ENTREZID PATHID
1 3855 R-HSA-1266738
2 3855 R-HSA-6805567
3 3855 R-HSA-6809371
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] reactome.db_1.59.1 AnnotationDbi_1.38.0 IRanges_2.10.0
[4] S4Vectors_0.14.0 Biobase_2.36.2 BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] compiler_3.4.0 DBI_0.6-1 memoise_1.1.0 Rcpp_0.12.10 RSQLite_1.1-2
[6] digest_0.6.12
