June Changes in BioC Devel
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July 2007
affy
ReadAffy constructs AnnotatedDataFrame rather than calling
read.AnnotatedDataFrame; minor doc fixes
affyio
fix an issue in read_bpmap with SET_VECTOR_ELT()
affylmGUI
References to Digestion changed to Degradation. Changed
Menu Item name and function names. See Bioconductor emails
from Gordon Smyth/Robert Gentleman around December
6th. 2006.
Fixed a bug in Normalize.R introduced in 1.10.1 - bracket
misplaced as shown below: Replaced this line
Try(write.table(NormalizedAffyData.exprs),file=FileName,
sep="\t",quote=FALSE,col.names=NA) with
Try(write.table(NormalizedAffyData.exprs,file=FileName,
sep="\t",quote=FALSE,col.names=NA))
Error on console when HTML report was to be created. It
read: "Error in get(x, envir, mode, inherits) : variable
"HTMLenv" was not found" Modify htmlreport.R replace:
try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir =
.GlobalEnv))) with: if
(exists("HTMLenv",where=".GlobalEnv",mode="environment")){
try(assign(".HTML.graph", TRUE, env = get("HTMLenv", envir =
.GlobalEnv))) }#end of if
(exists("HTMLenv",where=".GlobalEnv",mode="environment"))
annaffy
replaced hgu95av2db by hgu95av2.db
Fix ann pkg detection for name change in SQLite-based packages
annotate
Updates for SQLite-based package rename db => .db
AnnotationDbi
Fixed broken example in ?GONode.
The rightColType slot for ENTREZID map is not set to
"integer" anymore (this slot should probably go away for
AnnDbMap objects since it seems that left names and right
names should always be strings if we want revmap() and the
upcoming "plug map" feature to work properly and in a
consistent manner)
Replaced "db" suffix by ".db" in all db package names. Small
improvements to makeAnnDbPkg()
Added experimental agilent package.
Package should look a lot like an hgu95av2.
This is because its using a similar set of
operations to knit everything together as
is used by that package. So it *should* work
as one of these.
Fixed bug in dbCountUniqueMappedVals(). Added debug.sql().
Added loadAnnDbPkgIndex() and use it in
"makeAnnDbPkg-character" method. Reorganized
ANNDBPKG-INDEX.TXT.
beadarray
backgroundCorrect() function now checks if background
correction has already been carried out before doing any
further adjustment - imageplot() now allows negative values
to be displayed (previously only plotted non-negative
values). Also gives a warning when NA/Inf values are
present. These are values are replaced with zeros - bug in
readIllumina() which meant background correction was not
taking place when useImages=FALSE now fixed
plotDERank now returns a matrix.
Biobase
Add assayData documentation to ExpressionSet - reference
eSet, where info on subsetting also provided - add [[
documentation for AssayData
added "strbreak" to the show method for AnnotatedDataFrame
Provide more consistent AnnotatedDataFrame dimLabels for
eSet
Completed C-implementation of the Needleman-Wunsch algo
(src/align_needwunsQS.c). Depending on the size of the
strings to align, the new needwunsQS() function is 100 to
1000 times faster than the old one (pure R). Also, now
needwunsQS() returns a BStringAlign object (new class which
purpose is to describe an alignment between 2
strings). Deprecated alignScore() in favor of score(). Still
need to update needwunsQS() man page and to document new
BStringAlign-related methods (initialize, align1, align2,
score, show).
added nucleotide alignment example in needwunsQS() man page
added the complementViews() function + a split() method for
BString objects (will probably use another name for the
latter since there is some uglyness associated to the use of
the split() generic)
Renamed "complementViews" -> "mask" + mask() is now a
generic with methods for BString and BStringViews
objects. Some other minor (internal) changes.
Biostrings
added src/align_needwunsQS.c
some work on src/align_needwunsQS.c
more work on src/align_needwunsQS.c
Completed C-implementation of the Needleman-Wunsch algo
(src/align_needwunsQS.c). Depending on the size of the strings
to align, the new needwunsQS() function is 100 to 1000 times
faster than the old one (pure R). Also, now needwunsQS() returns
a BStringAlign object (new class which purpose is to describe an
alignment between 2 strings). Deprecated alignScore() in favor
of score(). Still need to update needwunsQS() man page and to
document new BStringAlign-related methods (initialize, align1,
align2, score, show). Version bump anymway.
Depends on R (>= 2.6.0) + some cosmetic.
added nucleotide alignment example in needwunsQS() man page
changed size limit for length(s1)*length(s2) from 1e+08 to 4e+08
in needwunsQS()
Added predefined scoring matrices BLOSUM45, BLOSUM50, BLOSUM62,
BLOSUM80, BLOSUM100, PAM30, PAM40, PAM70, PAM120 and
PAM250. Removed blosum50. See ?scoring_matrices - Arg
'substmat' for needwunsQS() can now be the name of a predefined
scoring matrix (e.g. "BLOSUM62"). - BStringAlign class: added
"length", "nchar" and "alphabet" methods + a man page. -
Version bump.
added the complementViews() function + a split() method for
BString objects
(will probably use another name for the latter since there is
some uglyness associated to the use of the split() generic)
Renamed "complementViews" -> "mask" + mask() is now a generic
with methods for BString and BStringViews objects. Some other
minor (internal) changes. Version bump.
Some minor bug fixes. Updated TODO (moved some comments about
"normalized" BStringViews objects from TODO to
R/BStringViews-constructors.R).
Got rid of the "split" generic by merging the "split"
functionality to the "mask" generic. "mask" has now a dedicated
man page. Version bump.
Reorganized/improved the set of functions used for fast
substring extraction.
Added some examples to man page for fast substring
extraction. Version bump.
renamed subBStringViews -> subviews
BufferedMatrix
add MoveStorageDirectory()
Category
Use exact=TRUE in calls to [[ This resolves undesired partial
matching that was occuring in addChrBandAnnotation.
Fix gseaperm to work properly in absence of the Matrix
package
cellHTS
The function "normalizedChannels" was restored to the
behaviour it had before May 2007, and a new function called
"summarizeChannels" was added. The "path" argument similar
to that in function "readPlateData" was added to the
functions "configure" and "annotate". In "writeReport", the
option to add the tooltips to the image plot was set by
default to FALSE.
Corrected for the case where there are different batches
using different positive controls.
cellHTS2
A completely revised (from scratch) implementation of cellHTS
To avoid too many tears from existing users, we give it a
new name, so they know they are in for some changes when
they install it. Eventually, cellHTS can be taken out of
the releases.
EBImage
bug correction in moments for the case when image does not
contain any objects
fbat
fixed a bug in checkMarkers so that allele frequencies can
be calculated correctly.
added 'drop=FALSE' for some R code to avoid converting
matrix to vector.
added a argument 'missingOutput' to the functions
'pedAFreq' and 'pedGFreq' to fix a bug that caused wrong
output of the functions 'pedAFreq', 'pedGFreq' and
'checkMarkers'. If 'missingOutput=TRUE', then information
about missing alleles will output, otherwise missing allele
information will not be output.
introduced a pedigree object containing four elements
'ped', 'columns', 'markerNames', and 'Position'.
added functions 'readPed', 'readLink', and 'readHapMap' to
read pedigree file, data file with PLINK format, and snp
files output by HapMap webbrowser to a pedigree object
added the functions 'checkMarkers.default' and 'getFounders'
added sample info files for subjects in four races (CEU,
YRI, CHB, and JPT) in HapMap studies.
deleted CAMP example files (because GeneticsBase package has
these files) moved geneSet2Ped code to GeneticsBase
genefilter
Remove require.SYMBOL arg from nsFilter, add ... to generic
require.SYMBOL may make sense for display purposes, but
does not make sense as a gene filtering option since lack of
symbol has no biological interpretation.
... was added to the nsFilter generic to give more
flexibility to specializing methods.
GeneticsBase
introduced pedigree object containg five elements (ped,
columns, markerNames, Position, fileName) in the function
ped2geneSet
Moved geneSet2Ped files from fbat to GeneticsBase
deleted power.casectl.R which is no longer used
GEOquery
Added GSEMatrix argument to getGEO to allow parsing of
SeriesMatrix GSE files Changed GPL parsing to be much
faster; other entities to follow
GlobalAncova
Import AnnotationDbi The generics for accessing GO objects
moved to AnnotationDbi. The addition of the package to
Depends is hopefully temporary, but allows passing of check
for now.
globaltest
Add AnnotationDbi to Depends generic functions for
manipulating GO objects moved to AnnotationDbi. Although it
should be possible to only import, that doesn't appear to be
working. For now, import _and_ Depend.
GOstats
Fix a bug in termGraphs reverseEdgeDirections doesn't handle
edge attributes properly yet so we do the reversing as a
last step.
Fix node labeling in termGraphs and plotGOTermGraph
graph
This is an >= R-2.6.0 package now
Remove call to addVigs2WinMenu from Biobase This causes a
warning because we don't want to depend/suggest
Biobase. Although adding the menu item is a good thing, we
hope alternatives will be available and common in R 2.6.0
Deprecated buildRepDepGraph and pkgInstOrder Both functions
have more powerful equivalents available in the pkgDepTools
package. Once removed, the Suggest on RBGL may be able to be
removed. The import for tools can be as well.
subGraph for graphNEL now properly propagates node and edge
attributes
minor fixes to the graph vignette and a rewrite of the
design discussion
introduced the start of some multigraph classes
idiogram
idiogram visuals improved - telomere tips and hashed
centromere.
added a "color.cen" option to idiogram - allows you to
change the color of the centromere when margin="i"
keggorth
New Package:
graph support for KO, KEGG Orthology
Maintainer:
Vince Carey
limma
- new argument n.pts for normexp.fit. n.pts=2^10 becomes the
default for method="normexp" in backgroundCorrect(). This
decreases computation time and introduces some robustness.
- backgroundCorrect() now accepts a matrix argument.
- decideTests(method="hierarchical") now passes the
adjust.method down to the second (t-test) level of
testing. Previously the second level testing was always
"holm". The spelling is also corrected from "heirarchical"
to "hierarchical".
logicFS
Fixed a bug that occurs when in the multiple tree case not
all logic trees are grown.
lumi
Adding code of checking negative values when using log2
transform.
Major updates:
1. All the major functions compatible with both ExpressionSet and
LumiBatch class
2. presentCount was removed from the featureData. use
detectionCall function to estimate presentCount
3. lumiR function now allows user to select the input data
columns
4. Add lumiB function for background correction
5. lumiExpresso function to encapsulate all preprocessing
functions
6. Vignette tutorial has major updates.
made4
bug update to heatplot, added arraylabels to ord
makecdfenv
Added a message at the end of make.cdf.package() telling end
user that they have to install the package before they can
use it.
Added just a bit more to the message for make.cdf.package,
pointing users to make.cdf.env if they don't want to install
a package.
oneChannelGUI
Fixing a bug related to the load of Rat exon arrays. Fixing a
but related to the load of exon data using APT tools Adding
the clustering menu also the raw affy menu Adding PCA with
in the classification tools
Interface to APT tools DABG p-value calculation was
implemented. Interface to APT tools MiDAS method for
alternative splicing detection was implemented.
filteringMidas function was implemented in order to selected
putative alternative splicing using MiDAS p-values.
oneChannelGUI was adapted to the modifications made in
affylmGUI
Adding MiDAS functions
Adding brief Hs annotation data derived by Affymetrix
data. This annotation file will be available until
annotation libraries for exon arrays will be available
Exon arrays analysis: Fixing a bug in the function filtering
gene/exon expression on the basis of dabg p-value Adding a
new set of functions to perform basic files manipulation
within oneChannelGUI Exon arrays analysis: Adding hs gene
level annotation to limma TopTable. TopTable annotation is
now done using bioconductor annotation libraries for 3'IVT
afymetrix arrays
Linking Hs core exon annotation to data generated with APT
tools as weel as with those generated with Expression
Console
Adding RankProd interface Fixing APT MiDAS DABG
implementations
Adapting the target file to the use of RPadvance
Alternative splicing detection by rank product method was
implemented (The efficacy of the method is still under
evaluation). RP and RPAdvance functions from the RanKProd
package were gaphically interfaced in opneChannelGUI.
panp
Changed pa.calls() to support new ExpressionSet object as
input. Changed pa.calls() output object to list of two
matrices (was exprSet). pa.calls() can still accept exprSet
input object, but will throw warning message. Removed
extraneous test exprSet. Single test dataset is now an
ExpressionSet.
pcaMethods
Applied Kevin Wrights diff for faster nipals. Nipals PCA
really should be re-written in C for further speed
improvement
pdInfoBuilder
Update DB_PATH in .onLoad for pd.mapping template
If the user has different versions installed in multiple
package libraries, we need to get the right one at
runtime. Note that for the lazyloading mechanism to work and
so that we can create a valid map object, we also need the
path in package scope for the initial install.
Add templated unit test suite for pdInfo packages
Thanks to a patch from Vince, packages generated by
pdInfoBuilder now include a minimal RUnit unit test suite.
preprocessCore
Added R_qnorm_robust_weights to the roaster of C callables
so that affyPLM can actually use it (without this, affyPLM
does not compile on Windows).
Added med_abs to the roaster of C callables (same as for
R_qnorm_robust_weights in previous commit.
Ringo
enabled addition of probes' GC content to probeAnno
environment
Rintact
remove slots interactionType, expPubMed and expIntAct from
class interactionEntry, and add them to
intactInteraction. This changes allow uses map interactions
with experiment and interaction detaction methods when one
interactionEntry contains multiple experiments. Also
modified function psi25complex to provide protein complex
IntAct ID in the outputs.
Ruuid
Refactor to minimize the WIN32 specific code
Use RAWSXP instead of CHARSXP to handle uuid data This patch
makes Ruuid compatible with recent changes in R 2.6.0
siggenes
Improved version of denspr (which is used in ebam for
categorical variables).
Fixed a few bugs. Now lev in cat.ebam and cat.stat can
also handle lists.
Now RefSNP IDs can be added to the html output.
sigPathway
Added functions (e.g., importGeneSets) to let users import
gene sets stored in GMT, GMX, GRP, and XML file formats.
vsn
fixed a bug in show method for "vsn", and clarified a man
page
Now the parameters for optim (factr, pgtol) are no longer
hardcoded, but are passed down from R and are taken from the
vsnInput object
Better comment on prototype vsnInput In preceding revision,
I mistakenly checked in an edited version of vsn.c. I have
reverted this back to how it was before.
Now the L-BFGS-B parameters are exposed
xcms
Added wrapper for MassSpecWavelet peak picking on single
spectra (findPeaks.MSW) Added some more logic to
joinOverlappingFeatures()