User: l.nilse
l.nilse • 0
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Posts by l.nilse
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Comment:
C: Uniprot.ws getting Function [CC]
... Great. Thanks for the fix, James. We will test and then close the GitHub issue.
...
written 15 months ago by
l.nilse • 0
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Comment:
C: Uniprot.ws getting Function [CC]
... Thanks, James. - I filed a features request. https://github.com/Bioconductor/UniProt.ws/issues/1
...
written 15 months ago by
l.nilse • 0
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Comment:
C: Uniprot.ws getting Function [CC]
... See column Function [CC] here.
https://www.uniprot.org/help/uniprotkb_column_names
...
written 15 months ago by
l.nilse • 0
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... UniProt.ws library is a great tool which we are using extensively. With
db <- UniProt.ws(taxId=9606)
I can read the database for one specific species. How can I generate a database for two species
db <- UniProt.ws(taxId=c(9606,10090))
or how can I combine two databases to a single one? Tha ...
written 21 months ago by
l.nilse • 0
• updated
21 months ago by
James W. MacDonald ♦ 50k
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... Here a possible solution complete with an example. Note that there are duplicate entries in the keys and multiple KEGG results.
library(UniProt.ws)
species <- 9606 # homo sapiens
up <- UniProt.ws(taxId=species)
UniqueSpaceSeparated <- function(x) {
u <- unique(x)
r <- paste ...
written 2.7 years ago by
l.nilse • 0
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... Together with match() this is a nice solution. Avoids me calling select() multiple times.
Thanks a lot for this, Jim and Martin.
...
written 2.7 years ago by
l.nilse • 0
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... My UNIPROT keys are not necessarily unique (in your example they are: Q12345, R4543, T96874), i.e. split/collapse will not work.
I had hoped for a multiVals parameter (first, CharacterList, ...) in select() as is available in the mapIds() interface. https://bioconductor.org/packages/release/bioc/ht ...
written 2.7 years ago by
l.nilse • 0
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... I am using UNIPROTKB keys to retrieve KEGG entries. Often multiple KEGG entries are found for the same key, resulting in a select() result with more rows than keys.
'select()' returned 1:many mapping between keys and columns
Is it possible to get multiple KEGG entries in the same row, i.e. number ...
written 2.7 years ago by
l.nilse • 0
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2.7 years ago,
created an answer that has been accepted.
For A: UniProt.ws report 1:many mappings in a single row
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