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Bioconductor Changlog.
Tue, 13 Oct 2009
biomaRt
Added a missing print.
Nicer formatting.
I added some more explanation to the NP2009code man page.
Also, two defunct messages (martDisconnect, connect) are a bit more
explicit.
Fixed bug with boolean filters
biomaRt
Added getBMlist function to get list output format
minor fix
New release of biomaRt. Supports web service only functions as this is the only way of communication supported by the BioMart suite. Older MySQL based functionality will be supported in an alternate package which will be added soon.
biomaRt
Ensembl update to version 47
biomaRt
Just a quick fix to restore functionality to example(getGene)
Inside checkWrapperArgs(), martFilters(mart) is now returning
something other than what it used to. Now its a dataframe which is
not easily coerced to a list. listFilters() still works the same
though and can also work here in our pinch. So that is what it does
for now to restore functionality.
biomaRt
Update to fix gene symbol attribute and filter names in Ensembl human and mouse datasets
biomaRt
updated vignet
biomaRt
I tried to make getBM return a somewhat more useful error message,
and added FIXMEs.
biomaRt
Update of DESCRIPTION file
Archives of the Ensembl database are now available using biomaRt in web service mode. listMarts(archive=TRUE) will display all the available archives. Updated Vignette with an example to access Ensembl archives
biomaRt
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
biomaRt
Provided stubs for old functions
Provided stubs for old functions
biomaRt
update for np
biomaRt
Update of DESCRIPTION file
biomaRt
I made the getBM function behave more consistently (and without
causing an error in certain cases) - see also my email to Steffen of
today.
biomaRt
Provided stubs for old functions
biomaRt
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
biomaRt
fixed up calls to xmlSApply so that the function was not quoted - but
biomaRt
Removed deprecated function getFeature as getBM is a more general function to do these types of queries. Added some extra argument checking for useMart, filterOptions and filterType functions.
biomaRt
removed quotes from do.call
biomaRt
Deprecated the getSNP, getHomolog and getAffyArrays functions as these queries can be performed better by the getBM, getLDS and listFilters functions respectively.
biomaRt
Changes to listFilters and its man page:
- give a better error message if "what" is invalid
- tell people that "group" is defunct.
biomaRt
Added INTERPRO example to the vignette
biomaRt
fixed up the RCurl infelicity - should now be clear
biomaRt
Removed getSNP, getHomolog, getAffyArrays as these functions are replaced by getBM and getLDS
biomaRt
Updated getSequence example
biomaRt
minor fix for unnecessary braces warning of CMD check
biomaRt
Fixed Rnw
biomaRt
Update for use of biomaRt in MySQL mode. Ensembl changed the port of the current database release and this needed a fix.
biomaRt
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
biomaRt
Restored access to archives
biomaRt
Fixed issue with new database port to ensembl, for use of biomaRt in MySQL mode
test
biomaRt
RG moved the RCurl dependence into an import so that RCurl is
no longer on the search path