CHANGES IN VERSION 1.10.3 ------------------------- o Update dunkley2006params <2016-04-01 Fri> CHANGES IN VERSION 1.10.2 ------------------------- o Update dunkley2006params <2016-03-30 Wed> CHANGES IN VERSION 1.10.1 ------------------------- o Internally using MartInterface to query individual mart servers to bypass the biomart.org downtime <2015-12-09 Wed> (ported from devel) o Update params data objects <2015-12-16 Wed> CHANGES IN VERSION 1.10.0 ------------------------- o Bioc release version 3.2 CHANGES IN VERSION 1.9.7 ------------------------ o New SpatProtVis visualisation class <2015-08-13 Thu> o add link to explanation of supportive/uncertain reliability scores in tl vignette <2015-09-02 Wed> CHANGES IN VERSION 1.9.6 ------------------------ o Update REAMDE with TL ref o Update refs in lopims documentation <2015-07-30 Thu> CHANGES IN VERSION 1.9.5 ------------------------ o update doc <2015-07-15 Wed> CHANGES IN VERSION 1.9.4 ------------------------ o Add reference to TL paper and link to lpSVM code <2015-07-06 Mon> o highlightOnPlot throws a warning and invisibly returns NULL instead of an error when no features are in the object <2015-07-08 Wed> o highlightOnPlot has a new labels argument <2015-07-10 Fri> CHANGES IN VERSION 1.9.3 ------------------------ o Clarify error when no annotation params are provided <2015-05-11 Mon> o support for matrix-encoded markers <2015-05-19 Tue> o New default in addLegend: bty = "n" <2015-05-20 Wed> o getMarkers now supports matrix markers <2015-05-20 Wed> o getMarkerClasses now supports matrix markers <2015-05-20 Wed> o markerMSnSet and unknownMSnSet now support matrix markers <2015-05-20 Wed> o sampleMSnSet now supports matrix markers <2015-05-23 Sat> o updated yeast markers and added uniprot ids <2015-05-27 Wed> o plot2D support a pre-calculated dim-reduced data matrix as method parameter to avoid recalculation <2015-05-27 Wed> CHANGES IN VERSION 1.9.2 ------------------------ o Lisa's colour palette <2015-05-08 Fri> CHANGES IN VERSION 1.9.1 ------------------------ o new plot2Ds function to overlay two data sets on the same PCA plot [2015-04-17 Fri] o regenerate biomart data used by setAnnotationParams [2015-04-24 Fri] o new setStockcolGui function to set the default colours manually via a simple interface [2015-04-29 Wed] o new move2Ds function to produce an transition movie between two MSnSets [2015-04-29 Wed] o functions to convert GO ids to/from terms. See ?goTermToId for details <2015-05-08 Fri> CHANGES IN VERSION 1.9.0 ------------------------ o new devel version for Bioc 3.2 CHANGES IN VERSION 1.7.13 ------------------------- o use donttest instead of dontrun [2015-04-09 Thu] CHANGES IN VERSION 1.7.12 ------------------------- o don't run knntl example to reduce checking time and timeout on Windows [2015-04-08 Wed] CHANGES IN VERSION 1.7.11 ------------------------- o fix splitTh, closes issue #49 [2015-04-06 Mon] CHANGES IN VERSION 1.7.10 ------------------------- o Change in vignette to work on zin1: using 12 random th rows. See issue #49 for details. Fixed in version 1.7.11. [2015-04-03 Fri] CHANGES IN VERSION 1.7.9 ------------------------ o updated tl vignette [2015-04-02 Thu] o depending on latest (1.5.8) pRolocdata [2015-04-02 Thu] CHANGES IN VERSION 1.7.8 ------------------------ o updating tl vig [2015-04-02 Thu] o update getParams documentation [2015-04-02 Thu] CHANGES IN VERSION 1.7.7 ------------------------ o renaming theta.scores to knntl.scores [2015-03-24 Tue] CHANGES IN VERSION 1.7.6 ------------------------ o added the theta inductive transfer infrastructure [2015-02-05 Thu] o theta vignette stub [2015-02-06 Fri] o rename getClasses to getMarkerClasses [2015-02-06 Fri] o added the infrastructure to create GO MSnSet [2015-02-07 Sat] o Fixed ml vignette [2015-02-16 Mon] o new filterZeroRows function [2015-03-10 Tue] o hpa data section [2015-03-10 Tue] o theta sections [2015-03-10 Tue] o deprecate getRegulari[z|s]edParams [2015-03-11 Wed] CHANGES IN VERSION 1.7.5 ------------------------ o Fix vignettes: run bibtex and pdflatex twice and typo [2015-02-03 Tue] CHANGES IN VERSION 1.7.4 ------------------------ o Use default Sweave call to build vignette [2015-01-24 Sat] CHANGES IN VERSION 1.7.3 ------------------------ o use Biocstyle [2015-01-23 Fri] o replace library/require by requireNamespace [2015-01-23 Fri] CHANGES IN VERSION 1.7.2 ------------------------ o added t-SNE method to plot2D [2015-01-14 Wed] o Updated NAMESPACE imports [2015-01-14 Wed] CHANGES IN VERSION 1.7.1 ------------------------ o updated vignettes with markers.orig [2014-10-30 Thu] o updated ml tests [2014-10-30 Thu] CHANGES IN VERSION 1.7.0 ------------------------ o new devel version, Bioc 3.1 CHANGES IN VERSION 1.6.0 ------------------------ o new stable version, Bioc 3.0 CHANGES IN VERSION 1.5.19 ------------------------- o added Video tag in DESCRIPTION [2014-10-07 Tue] CHANGES IN VERSION 1.5.18 ------------------------- o HUPO 2014 poster [2014-01-02 Thu] CHANGES IN VERSION 1.5.17 ------------------------- o fix 'replacing previous import by MLInterfaces::plot when loading pRoloc' warning by using specific importFrom [2014-09-27 Sat] CHANGES IN VERSION 1.5.16 ------------------------- o new pRolocGUI section [2014-08-15 Fri] o new foi section [2014-08-16 Sat] CHANGES IN VERSION 1.5.15 ------------------------- o svmOpt sigma defaults changed from 10^(-2:3) to 10^(-3:2) [2014-08-15 Fri] o in xxxOptimisation, the best parameter(s) for the validation classification runs are now chosen at random instead of using the first best param (see change in pRoloc:::getBestParam that got a sample argument defaulted to TRUE) [2014-08-15 Fri] o When calculating macroF1 scores (xval and validation), NAs are set to 0 (via MLInterfaces:::.macroF1(..., naAs0 = TRUE)). The macro F1 will not be NA (when mean of F1s is calculated) but lowered. This avoids having an NA macro F1 when 1 (or more) classe(s) end(s) up with NA (also set to 0) precision(s) or recall(s) [2014-08-15 Fri] CHANGES IN VERSION 1.5.14 ------------------------- o add title to plotDist figures [2014-08-13 Wed] CHANGES IN VERSION 1.5.13 ------------------------- o none CHANGES IN VERSION 1.5.12 ------------------------- o support mirrorX/mirrorY in highlightOnPlot [2014-07-22 Tue] CHANGES IN VERSION 1.5.11 ------------------------- o Remove plot2D outliers param [2014-07-10 Thu] o fix subsetAsDataFrame for keepColNames and write unit test [2014-07-11 Fri] CHANGES IN VERSION 1.5.10 ------------------------- o alias lopims4 function [2014-07-01 Tue] CHANGES IN VERSION 1.5.9 ------------------------ o Export single steps of lopims [2014-06-23 Mon] o Rephrase classifier parameter optimisation proceudres [2014-06-23 Mon] CHANGES IN VERSION 1.5.8 ------------------------ o nndistx_matrix function added to allow use of query matrix when calculating knn distances [2014-06-18 Wed] o nndist[x]_[matrix|msnset] are now available using the experted nndist method [2014-06-18 Wed] o markerSet and unknownSet renamed to markerMSnSet and unknownMSnSet [2014-06-19 Thu] o functions sampleMSnSet and testMSnSet added [2014-06-19 Thu] o fix keepColNames in pRoloc:::subsetAsDataFrame - fcol was always renamed to "markers" [2014-06-19 Thu] CHANGES IN VERSION 1.5.7 ------------------------ o add recommended biocView [2014-06-05 Thu] CHANGES IN VERSION 1.5.6 ------------------------ o addMarkers has a new mcol argument to set the markers feature variable label [2014-05-29 Thu] CHANGES IN VERSION 1.5.5 ------------------------ o replaced MSVBAR::rmultnorm with mvtnorm::rmvnorm since the former has been removed from CRAN and don't import [2014-05-21 Wed] o Bug tracking [2014-05-26 Mon] CHANGES IN VERSION 1.5.4 ------------------------ o testMarkers gets an error argument [2014-05-14 Wed] o plotDist now has a ylim argument [2014-05-21 Wed] CHANGES IN VERSION 1.5.3 ------------------------ o import all MLInterfaces [2014-04-30 Wed] o new param optim secion in ml vignette [2014-05-05 Mon] o various ml typos and pRolocmakers man update [2014-05-06 Tue] CHANGES IN VERSION 1.5.2 ------------------------ o In plotDist, ... is now passed to matlines instead of plot and has a new lty parameter [2014-04-17 Thu] o new highlightOnPlot function, using the new features of interest infrastructure [2014-04-29 Tue] CHANGES IN VERSION 1.5.1 ------------------------ o new dunkley2006 pdunit object created with mclust 4.3 [2014-04-08 Tue] o addMarker also accepts fcol and addMarkers unit test [2014-04-14 Mon] CHANGES IN VERSION 1.5.0 ------------------------ o Bioc devel 3.0 CHANGES IN VERSION 1.4.0 ------------------------ o Bioc release 2.14 CHANGES IN VERSION 1.3.19 ------------------------- o fixed error introduced with mclust 4.3 (that now returns the data in the Mclust output - see comment in pRoloc:::gmmOutliers for details) [2014-04-07 Mon] CHANGES IN VERSION 1.3.18 ------------------------- o getPredictions can take class-specific scores [2014-04-04 Fri] CHANGES IN VERSION 1.3.17 ------------------------- o fixed newly introduced bug (see 1.3.16) in pRoloc:::subsetAsDataFrame - thank you unit tests for saving me, again [2014-03-26 Wed] CHANGES IN VERSION 1.3.16 ------------------------- o pRoloc:::subsetAsDataFrame now preserved original sample/column names [2014-03-24 Mon] o fixed wrong message when using col and pch in plot2D [2014-03-25 Tue] CHANGES IN VERSION 1.3.15 ------------------------- o updated pRolocmarkers("mmus") [2014-03-21 Fri] o moved extdata/*csv to pRolocdata [2014-03-23 Sun] o using *csv from pRolocdata [2014-03-23 Sun] CHANGES IN VERSION 1.3.14 ------------------------- o deleted tab character [2014-03-15 Sat] o added support for GMM parametrisation to phenoDisco [2014-03-17 Mon] o message instead of warning when using colour and pch [2014-03-21 Fri] o remove 1 duplicated mouse marker [2014-03-21 Fri] CHANGES IN VERSION 1.3.13 ------------------------- o fixed a bug in addLegend [2014-03-14 Fri] o updated testing to testthat 0.8 [2014-03-14 Fri] o Fixing several warnings about symnbols being replaced upon pRoloc loading and note about usage of ::: [2014-03-15 Sat] CHANGES IN VERSION 1.3.12 ------------------------- o added phenoDisco2 for testing, allows choice of GMM parameters [2014-02-26 Wed] o removed duplicated fly markers [2014-02-28 Fri] o updated affiliations in vignettes [2014-03-10 Mon] CHANGES IN VERSION 1.3.11 ------------------------- o modify to new biocViews to DESCRIPTION file by s.arora [2014-03-04] CHANGES IN VERSION 1.3.10 ------------------------- o new phenoDisco ndims argument to use more than two two principal components as input for discovery analysis [2014-01-03 Mon] o fixed and updated phenoDisco logging [2014-02-03 Mon] o added support for parallel phenoDisco execution. See BPPARAM argument [2014-02-03 Mon] o fixed issues with using PD and ndims [2014-02-10 Mon] o fixed call to anyUnknown in PD code [2014-02-10 Mon] o checking if duplicated markers in addMarkers [2014-02-14 Fri] CHANGES IN VERSION 1.3.9 ------------------------ o bump to force rebuild for new Rcpp CHANGES IN VERSION 1.3.8 ------------------------ o Removed trailing space in mmus nucleus markers [2014-01-21 Tue] o using filterNA to remove features with missing values in plot2D [2014-01-21 Tue] o fixed plot2D/addLegend [2014-01-23 Thu] CHANGES IN VERSION 1.3.7 ------------------------ o fixed addLegend to use correct colours (order) [2014-01-20 Mon] o fix typo in addMarkers man [2014-01-20 Mon] o re-arranged stockpch so that interleave full and empty plotting character [2014-01-20 Mon] 0 Removed last stockcol (tomato), too cose to "#FF7F00" [2014-01-20 Mon] CHANGES IN VERSION 1.3.6 ------------------------ o updated human markers: keep new pd.markers phenotypes, validated by Lisa and remove singletons [2014-01-14 Tue] o first stockpch is noe 19 [2014-01-16 Thu] o plot2D(.., pch) now taken into account for labelled data [2014-01-16 Thu] o removed alpha plot2D argument [2014-01-17 Fri] o updated plot2D and addLegend function with support for more organelle groups than colours. The previous versions are available as plot2D_v1 and addLegend_v1. [2014-01-17 Fri] CHANGES IN VERSION 1.3.5 ------------------------ o pRoloc citation [2014-01-12 Sun] CHANGES IN VERSION 1.3.4 ------------------------ o new unknownSet function [2013-12-11 Wed] o updated vignettes to account for tan2009r1 changes [2013-12-16 Mon] CHANGES IN VERSION 1.3.3 ------------------------ o update citation in phenoDisco.Rd [2013-11-22 Fri] o typos in vignettes [2013-11-25 Mon] CHANGES IN VERSION 1.3.2 ------------------------ o new markers [2013-11-06 Wed] o markers in vinette [2013-11-15 Fri] o mouse markers [2013-11-18 Mon] CHANGES IN VERSION 1.3.1 ------------------------ o using combineFeatures(..., na.rm=TRUE) in lopims pipeine [2013-10-22 Tue] o corrected spelling errors in phenoDisco doc [2013-10-29 Tue] CHANGES IN VERSION 1.3.0 ------------------------ o next devel version fot Bioc 2.14 CHANGES IN VERSION 1.1.8 ------------------------ o semi-sup and sup comparison sections in ml vig [2013-10-09 Wed] CHANGES IN VERSION 1.1.7 ------------------------ o getMarkers has names arg [2013-10-01 Tue] CHANGES IN VERSION 1.1.6 ------------------------ o new outliers arg to plot2D [2013-09-23 Mon] o cite addMarkers in vignette [2013-09-26 Thu] o add code chunk in poster vig [2013-09-26 Thu] CHANGES IN VERSION 1.1.5 ------------------------ o added biocViews [2013-09-19 Thu] o added knitr vig engine in ml [2013-09-19 Thu] o import dependencies [2013-09-20 Fri] CHANGES IN VERSION 1.1.4 ------------------------ o building ml vignette in Makefile [2013-09-11 Wed] CHANGES IN VERSION 1.1.3 ------------------------ o new private anyUnknown function, used in phenoDisco, to check for the presence of unlabelled ('unknown') data [2013-08-27 Tue] o added a note in vignette about "unknown" convention to define protein with unknown localisation [2013-08-28 Wed] o Added HUPO 2011 poster [2013-09-09 Mon] CHANGES IN VERSION 1.1.2 ------------------------ o fixed Author[s]@R [2013-05-16 Thu] o na.rm=TRUE in f1Count [2013-05-19 Sun] o added CITATION file [2013-06-07 Fri] o new testMarkers function [2013-06-29 Sat] o error message in getBestParams suggests to use testMarkers [2013-06-29 Sat] o nndist methods (see issue #23) [2013-07-01 Mon] o remove unnecessary as.matrix in plot2D's cmdscale [2013-07-19 Fri] o added plot2D(..., method = "MDS") example [2013-07-19 Fri] o changed 'euclidian' to 'euclidean' in nndist_matrix [2013-07-26 Fri] o fixed row ordering in phenoDisco, input and output rownames are now the same [2013-08-13 Tue] o Using filterNA in phenoDisco [2013-08-13 Tue] CHANGES IN VERSION 1.1.1 ------------------------ o Update README.md to reflect availability in stable release and biocLite installation [2013-04-07 Sun] o new MSe pipeline [2013-04-07 Sun] o perTurbo using Rcpp [2013-04-16 Tue] o initial clustering infrastructure (not exported) [2013-04-17 Wed] o new markerSet function [2013-04-24 Wed] o plsaOptim's ncomp is now 2:6 [2013-04-27 Sat] o added forword to vignette [2013-04-29 Mon] o default k is now seq(3, 15, 2) in knnOptim [2013-05-09 Thu] CHANGES IN VERSION 1.1.0 ------------------------ o Bioc 2.13 devel version bump CHANGES IN VERSION 1.0.0 ------------------------ o Bioc 2.12 stable version bump CHANGES IN VERSION 0.99.17 -------------------------- o illustrating class.weights in the vignette [2013-03-24 Sun] CHANGES IN VERSION 0.99.16 -------------------------- o new addMarkers function [2013-03-22 Fri] CHANGES IN VERSION 0.99.15 -------------------------- o Fixing issues in vignette [2013-03-22 Fri] CHANGES IN VERSION 0.99.14 -------------------------- o Added scale in tutorial [2013-03-02 Sat] o implemented viction [2013-03-09 Sat] o New vignette section on phenoDisco follow up classification [2013-03-19 Tue] o Using knitr engine [2013-03-19 Tue] CHANGES IN VERSION 0.99.13 -------------------------- o depending on MSnbase ]= 1.7.23 as makeNaData needs MSnbase:::nologging [2013-02-27 Wed] o updated phenoDisco parameters, added error messages when an insufficient number of markers per class and/or number of classes are used and updated phenoDisco help file [2012-02-28 Thu] o added first belief diffscores function [2013-03-01 Fri] CHANGES IN VERSION 0.99.12 -------------------------- o plot2D has gained a plot argument [2013-02-19 Tue] o new f1Count method [2013-02-20 Wed] o new makeNaData function [2013-02-20 Wed] o new makeNaData2 function [2013-02-21 Thu] o new whichNAfunction [2013-02-20 Wed] o updated tutorial vignette [2013-02-20 Wed] o Now passing ... to predictor functions in xxxClassification (reported by Marianne Sandin) [2013-02-26 Tue] CHANGES IN VERSION 0.99.11 -------------------------- o setUnknowncol(NULL) and friedns reset to default values [2013-02-19 Tue] CHANGES IN VERSION 0.99.10 -------------------------- o new default col/pch setters [2013-02-16 Sat] CHANGES IN VERSION 0.99.9 ------------------------- o Updates to phenoDisco: verbose param, fixed error in example, adding params to processingInfo [2013-02-11 Mon] o Unexported getOtherParams method [2013-02-12 Tue] o adding export param documentation [2013-02-12 Tue] CHANGES IN VERSION 0.99.8 ------------------------- o Integration of the perTurbo algorithms, contributed by Thomas Burger and Samuel Wieczorek [2013-01-18 Fri] o summariseMatList now has na.rm = TRUE by default [2013-01-19 Sat] o PerTurbo's inv/reg now as other hyperparams [2013-02-11 Mon] CHANGES IN VERSION 0.99.7 ------------------------- o knitr 1.0 compatibility [2013-01-15 Tue] o Updated phenoDisco documentation and README [2013-01-10 Thu] CHANGES IN VERSION 0.99.6 ------------------------- o removed updateClass man [2013-01-03 Thu] o removed old Rd files [2013-01-03 Thu] o Deprecating *Regularisation and *Prediction function [2013-01-03 Thu] o Updated new names in test_ml.R [2013-01-04 Fri] CHANGES IN VERSION 0.99.5 ------------------------- o more reg data into GenRegRes objects - cmMatrices (knn) [2012-11-15 Thu] (other) [2012-11-30 Fri] - testPartitions (knn) [2012-11-17 Sat] (other) [2012-11-30 Fri] o new minMarkers function [2012-11-16 Fri] o renamed updateClass to minClassScore [2012-11-16 Fri] o renamed xxxRegularisation to xxxOptimisation [2012-11-30 Fri] o renamed xxxPrediction to xxxClassification [2012-11-30 Fri] o renamed getRegularisedParams to getParams [2012-11-30 Fri] o moved exprsToRatios to MSnbase [2012-12-05 Wed] o updated phenoDisco help file [2012-12-07 Fri] o updated phenoDisco code to cope with identical protein profiles [2012-12-07 Fri] CHANGES IN VERSION 0.99.4 ------------------------- o Adding README file describing Rd generation and suggesting roxygen2 [2012-11-14 Wed] o Added scol=NULL to ignore completely [2012-11-14 Wed] CHANGES IN VERSION 0.99.3 ------------------------- o pdres in extdata - updated vignette [2012-11-14 Wed] o udpated pd's GS/times default [2012-11-14 Wed] CHANGES IN VERSION 0.99.2 ------------------------- o fixed MLearn("formula", "MSnSet", "clusteringSchema", "missing") - interface was wrong [2012-11-10 Sat] o vignette updates [2012-11-10 Sat] [2012-11-11 Sun] o nicer knn score names when scores = "all" [2012-11-11 Sun] CHANGES IN VERSION 0.99.1 ------------------------- o updated exprsToRatio when ncol(object) is 2 [2012-11-05 Mon] o typos in vignette [2012-11-09 Fri] [2012-11-10 Sat] o new MLearn method for signature c("formula", "MSnSet", "clusteringSchema", "missing") [2012-11-09 Fri] o Several vignette udpates [2012-11-10 Sat] CHANGES IN VERSION 0.99.0 ------------------------- o Submission to Bioc [2012-11-04 Sun]