Description Usage Arguments Details Value Author(s) Examples
Removing uninteresting GO terms from the list of terms relevant to a set
of UniProt accessions must be done manually. msarc.saveTerms
and
msarc.loadTerms
allow
the user to save the list of GO terms from a given msarc
object to
a file for manual filtering, then re-load the filtered file.
msarc.getTerms
and msarc.filterTerms
allow the user to retrieve
the list of GO terms as a data frame, filter it manually, and update the
msarc
object with the filtered list.
1 2 3 4 | msarc.saveTerms(msarc, filename="go_terms.txt")
msarc.loadTerms(msarc, filename="go_terms.txt")
msarc.getTerms(msarc)
msarc.filterTerms(msarc, keepers)
|
msarc |
an |
filename |
the name of a file to load from or save to. |
keepers |
a filtered data frame from |
The file generated by msarc.saveTerms
must be modified only by
having complete lines containing unwanted GO terms deleted.
msarc.getTerms
returns the list of GO terms as a data frame, with
columns for the GO ID, name of the category, and number of proteins in this
category. The user can filter this list manually, then use
msarc.filterTerms
to indicate which categories should be represented
in the final plot. msarc.filterTerms
is passed an msarc
object, and either a filtered data frame from msarc.getTerms
or a
vector of Uniprot IDs.
msarc.loadTerms
and msarc.filterTerms
return the modified
msarc
object.
msarc.saveTerms
returns nothing.
msarc.getTerms
returns a 3-column data frame: GO ID, GO category name,
count of the number of proteins that match this category.
Gord Brown
1 2 3 4 5 6 7 | data(sample_goterms,package="msarc")
## Not run: msarc.saveTerms(sample_goterms)
## Not run: sample_filtered <- msarc.loadTerms(sample_goterms,"terms.txt")
tbl <- msarc.getTerms(sample_goterms)
tbl <- tbl[c("GO:0017076","GO:0030554","GO:0032553","GO:0032555","GO:0032559",
"GO:0035639","GO:0036094","GO:0097159","GO:0017111","GO:0016462"),]
sample_filtered <- msarc.filterTerms(sample_goterms,tbl)
|
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