makeDbLinkTable.RdConstruct a table containing direct links to UniProt and AlphaFold pages for individual proteins.
makeDbLinkTable(
df,
idCol,
speciesCommon,
addSpeciesSpecificColumns = TRUE,
convTablePomBase = NULL,
convTableWormBase = NULL,
removeSuffix = TRUE,
signifDigits = 4
)data.frame with at least a column containing protein
identifiers (UniProt IDs).
Character scalar giving the column name of the column in
df containing protein identifiers. Each element of this
column should be a string, which can represent multiple protein IDs
separated by semicolons. See examples for an illustration.
Character scalar, providing the common species
name (e.g., "mouse", "roundworm", "fission yeast").
Logical scalar, indicating whether to add species-specific columns (whenever applicable).
Conversion table between UniProt IDs and
PomBase IDs. Only used if speciesCommon is
"fission yeast". A suitably formatted conversion table can be
generated using getConvTable(type = "PomBase").
Conversion table between UniProt IDs and
WormBase IDs. Only used if speciesCommon is "roundworm".
A suitably formatted conversion table can be
generated using getConvTable(type = "WormBase").
Logical scalar indicating whether suffixes of the
form -[0-9]+ should be removed from the protein ID before
generating the URL. Currently only influencing the AlphaFold,
ComplexPortal and BioGRID URLs.
Numeric scalar giving the number of significant digits
to round numeric columns to. If NULL, no rounding will be
performed.
A data.frame with database links for the proteins.
pbconv <- getConvTable(type = "PomBase")
makeDbLinkTable(data.frame(id = c("B5BP45", "O13282")), idCol = "id",
speciesCommon = "fission yeast",
convTablePomBase = pbconv)
#> id
#> 1 B5BP45
#> 2 O13282
#> UniProt
#> 1 <a href="https://www.uniprot.org/uniprot/B5BP45" target="_blank"> B5BP45</a>
#> 2 <a href="https://www.uniprot.org/uniprot/O13282" target="_blank"> O13282</a>
#> AlphaFold
#> 1 <a href="https://alphafold.ebi.ac.uk/entry/B5BP45" target="_blank"> B5BP45</a>
#> 2 <a href="https://alphafold.ebi.ac.uk/entry/O13282" target="_blank"> O13282</a>
#> ComplexPortal
#> 1 <a href="https://www.ebi.ac.uk/complexportal/complex/search?query=B5BP45" target="_blank"> B5BP45</a>
#> 2 <a href="https://www.ebi.ac.uk/complexportal/complex/search?query=O13282" target="_blank"> O13282</a>
#> BioGRID
#> 1 <a href="https://thebiogrid.org/search.php?search=B5BP45&organism=all" target="_blank"> B5BP45</a>
#> 2 <a href="https://thebiogrid.org/search.php?search=O13282&organism=all" target="_blank"> O13282</a>
#> PomBase
#> 1 <a href="https://www.pombase.org/gene/SPBC460.01c" target="_blank"> SPBC460.01c</a>
#> 2 <a href="https://www.pombase.org/gene/SPCC5E4.03c" target="_blank"> SPCC5E4.03c</a>
wbconv <- getConvTable(type = "WormBase")
makeDbLinkTable(data.frame(gid = c("eps-8", "epi-1"),
pid = c("Q7YTG1;O18250", "C1P641;C1P640")),
idCol = "pid", speciesCommon = "roundworm",
convTableWormBase = wbconv)
#> gid pid
#> 1 eps-8 Q7YTG1;O18250
#> 2 epi-1 C1P641;C1P640
#> UniProt
#> 1 <a href="https://www.uniprot.org/uniprot/Q7YTG1" target="_blank"> Q7YTG1</a>;<a href="https://www.uniprot.org/uniprot/O18250" target="_blank"> O18250</a>
#> 2 <a href="https://www.uniprot.org/uniprot/C1P641" target="_blank"> C1P641</a>;<a href="https://www.uniprot.org/uniprot/C1P640" target="_blank"> C1P640</a>
#> AlphaFold
#> 1 <a href="https://alphafold.ebi.ac.uk/entry/Q7YTG1" target="_blank"> Q7YTG1</a>;<a href="https://alphafold.ebi.ac.uk/entry/O18250" target="_blank"> O18250</a>
#> 2 <a href="https://alphafold.ebi.ac.uk/entry/C1P641" target="_blank"> C1P641</a>;<a href="https://alphafold.ebi.ac.uk/entry/C1P640" target="_blank"> C1P640</a>
#> ComplexPortal
#> 1 <a href="https://www.ebi.ac.uk/complexportal/complex/search?query=Q7YTG1" target="_blank"> Q7YTG1</a>;<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=O18250" target="_blank"> O18250</a>
#> 2 <a href="https://www.ebi.ac.uk/complexportal/complex/search?query=C1P641" target="_blank"> C1P641</a>;<a href="https://www.ebi.ac.uk/complexportal/complex/search?query=C1P640" target="_blank"> C1P640</a>
#> BioGRID
#> 1 <a href="https://thebiogrid.org/search.php?search=Q7YTG1&organism=all" target="_blank"> Q7YTG1</a>;<a href="https://thebiogrid.org/search.php?search=O18250&organism=all" target="_blank"> O18250</a>
#> 2 <a href="https://thebiogrid.org/search.php?search=C1P641&organism=all" target="_blank"> C1P641</a>;<a href="https://thebiogrid.org/search.php?search=C1P640&organism=all" target="_blank"> C1P640</a>
#> WormBase
#> 1 <a href="https://wormbase.org/species/c_elegans/gene/WBGene00001330" target="_blank"> WBGene00001330</a>
#> 2 <a href="https://wormbase.org/species/c_elegans/gene/WBGene00001328" target="_blank"> WBGene00001328</a>