Bioconductor Code: aroma.light

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# Version 3.31.1 [2023-06-30] ## Documentation * Update redirecting and broken URLs. * Fix `R CMD check` notes on "Escaped LaTeX specials: \&". # Version 3.31.0 [2023-04-25] ## Notes * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.18 for R (>= 4.4.0). # Version 3.30.0 [2023-04-25] ## Notes * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0). # Version 3.29.0 [2022-11-01] # Version 3.28.0 [2022-11-01] # Version 3.27.0 [2022-04-26] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.16 for R-devel. # Version 3.26.0 [2022-04-26] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.15 for R (>= 4.2.0). # Version 3.25.1 [2022-04-21] ## Bug Fixes * Fixed partial argument name used in `iwpca()`. # Version 3.24.0 [2021-10-27] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.14 for R (>= 4.1.1). # Version 3.23.1 [2021-08-19] ## Documentation * Update several citation URLs that were either broken or redirects elsewhere. # Version 3.22.0 [2021-05-19] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.13 for R (>= 4.0.3). # Version 3.20.0 [2020-10-27] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.12 for R (>= 4.0.0). # Version 3.18.0 [2020-04-27] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.11 for R (>= 3.6.1). # Version 3.17.1 [2019-12-09] ## Code Refactoring * Now importing `throw()` from **R.oo** instead of **R.methodsS3**. # Version 3.17.0 [2019-10-30] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.11 for R (>= 3.6.1). # Version 3.16.0 [2019-10-30] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.10 for R (>= 3.6.1). # Version 3.15.1 [2019-08-28] ## Bug Fixes * `wpca()` for matrices had a `length > 1 in coercion to logical` bug. # Version 3.15.0 [2019-05-02] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.10 for R (>= 3.6.0). # Version 3.14.0 [2019-05-02] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.9 for R (>= 3.6.0). # Version 3.13.0 [2018-10-30] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.9 for R (>= 3.6.0). # Version 3.12.0 [2018-10-30] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.8 for R (>= 3.5.0). # Version 3.11.2 [2018-09-04] ## Code Refactoring * `fitPrincipalCurve()` now requires **princurve** (>= 2.1.2) and was updated to make use of new `principcal_curve` class instead of deprecated `principcal.curve` class. This update "should not" affect the results, but see <https://github.com/rcannood/princurve/issues/8> for information of what has changed in the **princurve** package in this respect. # Version 3.11.1 [2018-08-28] * Updated installation instructions in README.md. # Version 3.11.0 [2018-04-30] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.8 for R (>= 3.6.0). # Version 3.10.0 [2018-04-30] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.7 for R (>= 3.5.0). # Version 3.9.1 [2017-12-19] ## New Features * `robustSmoothSpline()` now supports using Tukey's biweight (in addition to already exising L1) estimators. See argument `method`. Thanks to Aaron Lun at the Cancer Research UK Cambridge Institute for adding this feature. # Version 3.9.0 [2017-10-30] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.7 for R (>= 3.5.0). # Version 3.8.0 [2017-10-30] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.6 for R (>= 3.4.0). # Version 3.7.0 [2017-04-23] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.6 for R (>= 3.4.0). # Version 3.6.0 [2017-04-23] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.5 for R (>= 3.4.0). # Version 3.5.1 [2017-04-14] ## Significant Changes * `robustSmoothSpline()` uses a re-weighted re-iterative algorithm that fits a smooth spline using `stats::smooth.spline()`, calculates the residuals and which are used to fit a re-weighted smooth spline and so on until converence. Due to updates to `stats::smooth.spline()` in R (>= 3.4.0) it is no longer feasible to maintain a highly optimized version of the algorithm, because it was based on internal `stats::smooth.spline()` code that has no completely changed. Instead the re-iterative algorithm calls `stats::smooth.spline()` as is, which slows it down. More importantly, it will now give slightly different estimates. ## Software Quality * In addition to continous integration (CI) tests and nightly Bioconductor tests, the package is now also tested regularly against all reverse package depencies available on CRAN and Bioconductor. # Version 3.5.0 [2016-10-18] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.5 for R (>= 3.4.0). # Version 3.4.0 [2016-10-18] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.4 for R (>= 3.3.1). # Version: 3.3.0 [2016-05-03] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.4 for R (>= 3.3.0). # Version 3.3.2 [2016-09-16] ## Code Refactoring * Using `NA_real_` (not just `NA`) everywhere applicable. ## Bug Fixes * `robustSmoothSpline()` gave an error since R-devel (>= 3.4.0 r70682). # Version 3.3.1 [2016-08-10] ## Code Refactoring * CLEANUP: Using `seq_len()` and `seq_along()` everywhere (Issue #8) # Version 3.3.0 [2016-05-03] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.4 for R (>= 3.3.0). # Version 3.2.0 [2016-05-03] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.3 for R (>= 3.3.0). # Version 3.1.1 [2016-01-06] * Package requires R (>= 2.15.2). * CLEANUP: robustSmoothSpline() no longer generates messages that ".nknots.smspl() is now exported; use it instead of n.knots()" for R (>= 3.1.1). # Version 3.1.0 [2015-10-23] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.3 for R (>= 3.3.0). # Version 3.0.0 [2015-10-13] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.2 for R (>= 3.2.2). # Version 2.99.0 [2015-10-06] * No changes. # Version 2.9.0 [2015-09-17] ## Significant Changes * Argument `preserveScale` for `normalizeTumorBoost()` now defaults to FALSE. Since 1.33.3 (2014-04-30) it had no default and prior to that it was TRUE. # Version 2.5.3 [2015-09-13] ## Software Quality * ROBUSTNESS: Explicitly importing core R functions. ## Bug Fixes * `rowAverages()` and `normalizeAverages()` would give an error if some of the argument default functions are overridden by non-functions of the same name in the calling environment. # Version 2.5.2 [2015-06-16] ## Software Quality * Relaxed package test for `backtransformPrincipalCurve()`. # Version 2.5.1 [2015-05-24] * Bumped package dependencies. ## Deprecated and Defunct * Removed obsolete `wpca(..., method = "dsvdc")`; was only needed for backward compatibility with R (< 1.7.0). # Version 2.5.0 [2015-04-16] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.2 for R (>= 3.3.0). # Version 2.4.0 [2015-04-16] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.1 for R (>= 3.2.0). # Version 2.3.3 [2015-02-18] ## New Features * If a value of argument `xlim` or `ylim` for `plotDensity()` is NA, then it defaults to the corresponding extreme value of the data, e.g. `plotDensity(x, xlim = c(0, NA))`. # Version 2.3.2 [2015-02-17] ## Software Quality * ROBUSTNESS: Added package tests. Code coverage is 76%. ## Code Refactoring * CLEANUP: Using `requestNamespace()` instead of `request()`. # Version 2.3.1 [2014-12-08] * Same updates as in 2.2.1. # Version 2.3.0 [2014-10-13] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.1 for R (>= 3.2.0). # Version 2.2.1 [2014-12-08] ## Code Refactoring * Minor code cleanup. # Version 2.2.0 [2014-10-13] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.0 for R (>= 3.1.1). # Version 2.1.2 [2014-09-23] * Minor tweaks due to the move to GitHub. # Version 2.1.1 [2014-09-16] ## Software Quality * Fixed some new `R CMD check` NOTEs. ## Code Refactoring * CLEANUP: Now importing **R.utils** (instead of only suggesting it). * IMPORTANT/CLEANUP: The **matrixStats** package is no longer attached with this package. In other words, you now might have to add `library(matrixStats)` to your scripts. # Version 2.1.0 [2014-04-11] * The version number was bumped for the Bioconductor devel version, which is now Bioconductor 2.15 for R (>= 3.1.0). # Version 2.0.0 [2014-04-11] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 2.14 for R (>= 3.1.0). # Version 1.99.3 [2014-03-31] * Bumped the version such that the next release will be 2.0.0. # Version 1.33.3 [2014-03-30] ## Significant Changes * Argument `preserveScale` for `normalizeTumorBoost()` is now required. The goal with this is to in a future version migrate to use `preserveScale = FALSE` as the default (was `preserveScale = TRUE`) in order to avoid introducing a a global bias in the tumor allele B fraction of heterozygous SNPs. The examples use `preserveScale = FALSE` now. ## New Features * Added `pairedAlleleSpecificCopyNumbers()`. # Version 1.33.2 [2014-03-25] ## New Features * Now `plotDensity()` supports weights via argument `W`. # Version 1.33.1 [2014-03-25] ## New Features * Now `plotDensity()` also supports `density()` objects. ## Code Refactoring * CLEANUP: `robustSmoothSpline()` no longer uses `DUP = FALSE` in an internal `.Fortran()` call. * Bumped up package dependencies. # Version 1.33.0 [2013-10-14] * The version number was bumped for the Bioconductor devel version. # Version 1.32.0 [2012-10-14] * The version number was bumped for the Bioconductor release version, which is now Bioconductor 2.13 for R (>= 3.0.0). # Version 1.31.10 [2013-10-08] ## New Features * Added `averageQuantile()` for matrices in addition to lists. ## Performance * SPEEDUP: Now `normalizeQuantileSpline(..., sortTarget = TRUE)` sorts the target only once for lists of vectors just as done for matrices. ## Documentation * Merged the documentation for `normalizeQuantileSpline()` for all data types into one help page. Same for `plotXYCurve()`. ## Code Refactoring * Bumped up package dependencies. ## Bug Fixes * Argument `lwd` of `plotXYCurve(X, ...)` was ignored if `X` was a matrix. # Version 1.31.9 [2013-10-07] ## New Features * Now `library(aroma.light, quietly = TRUE)` attaches the package completely silently without any messages. * Now the `aroma.light` `Package` object is also available when the package is only loaded (but not attached). ## Documentation * Merged the documentation for `normalizeQuantileRank()` for numeric vectors and lists. * Now documention S3 methods under their corresponding generic function. # Version 1.31.8 [2013-10-02] ## Documentation * More generic functions are now "aliased" under relevant corresponding methods. # Version 1.31.7 [2013-09-27] ## Performance * SPEEDUP: Now all package functions utilizes **matrixStats** functions where possible, e.g. `anyMissing()`, `colMins()`, and `rowWeightedMedians()`. ## Code Refactoring * Bumped up package dependencies. # Version 1.31.6 [2013-09-25] ## Code Refactoring * CLEANUP: Package no longer use a fallback attachment of the **R.oo** package upon attachment. # Version 1.31.5 [2013-09-23] ## Software Quality * ROBUSTNESS: Now properly declaring all S3 methods in the NAMESPACE file. ## Performance * SPEEDUP/CLEANUP: `normalizeTumorBoost()` now uses `which()` instead of `whichVector()` of **R.utils**. Before R (< 2.11.0), `which()` used to be 10x slower than `whichVector()`, but now it's 3x faster. ## Code Refactoring * CLEANUP: Now only using `Authors@R` in DESCRIPTION, which is possible since R (>= 2.14.0). Hence the new requirement on the version of R. * Bumped up package dependencies. # Version 1.31.4 [2013-09-10] ## Software Quality * CLEANUP: Now package explicitly imports what it needs from **matrixStats**. ## Code Refactoring * Bumped up package dependencies. # Version 1.31.3 [2013-05-25] ## Performance * SPEEDUP: Removed all remaining `gc()` calls, which were in `normalizeQuantileSpline()`. * SPEEDUP: Replaced all `rm()` calls with NULL assignments. ## Code Refactoring * Updated the package dependencies. # Version 1.31.2 [2013-05-20] * Same updates as in v1.30.2. # Version 1.31.1 [2011-04-18] * Same updates as in v1.30.1. # Version 1.31.0 [2013-04-03] * The version number was bumped for the Bioconductor devel version. # Version 1.30.5 [2013-09-25] ## Software Quality * Backport from v1.31.5: Declaring all S3 methods in NAMESPACE. ## Code Refactoring * Backport from v1.31.5: `normalizeTumorBoost()` now uses `which()`, which also removes one dependency on **R.utils**. # Version 1.30.4 [2013-09-25] ## Software Quality * Backport from v1.31.4: Now package explicitly imports what it needs from **matrixStats**. # Version 1.30.3 [2013-09-25] ## Performance * Backport from v1.31.3: Removal of all `gc()` calls and removal of variables is now faster. ## Bug Fixes * Removed one stray `str()` debug output in `robustSmoothSpline()`. # Version 1.30.2 [2013-05-20] # Version 1.30.1 [2013-04-18] ## New Features * Now `backtransformPrincipalCurve()` preserves dimension names. ## Bug Fixes * `backtransformPrincipalCurve()` gave an error if the pricipal curve was fitted using data with missing values. * `fitPrincipalCurve()` would not preserve dimension names if data contain missing values. # Version 1.30.0 [2012-04-03] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.12 for R (>= 3.0.0). # Version 1.29.0 [2012-10-01] * The version number was bumped for the Bioconductor devel version. # Version 1.28.0 [2012-10-01] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.11 for R (>= 2.15.1). # Version 1.27.1 [2012-09-12] ## Software Quality * ROBUSTNESS: Replaced an `.Internal(psort(...))` call in `medianPolish()` with a call to **matrixStats**:::`.psortKM()`. # Version 1.27.0 [2012-08-30] ## Code Refactoring * CLEANUP: Removed `weightedMedian()`, which has been moved to the **matrixStats** package. * BACKWARD COMPATIBILITY: Now package depends on the **matrixStats** (>= 0.5.2) package, so that `weightedMedian()` is still available when loading this package. In future releases, **matrixStats** will be downgraded to only be a suggested package. # Version 1.26.1 [2012-08-30] ## Code Refactoring * Updated the package dependencies. ## Bug Fixes * `robustSmoothSpline()` would not work with most recent R devel versions. # Version 1.26.0 [2012-08-19] ## Significant Changes * Changed the license of aroma.light to GPL (>= 2) from LGPL (>= 2), because some of the implementation was adopted from GPL (>= 2) code, i.e. `robustSmoothSpline()` uses code from `stats::smooth.spline()`. ## Software Quality * `R CMD check` no longer warns about some examples depending on the **R.basic** package. # Version 1.25.4 [2012-08-19] ## Software Quality * WORKAROUND: Now `robustSmoothSpline()` robustly locates the proper native R fit function for smooth splines, which vary with different releases of R. # Version 1.25.3 [2012-04-16] ## Code Refactoring * Package no longer depends on **R.methodsS3**, only imports. # Version 1.25.2 [2012-04-16] ## Software Quality * `R CMD check` no longer complaints about `.Internal()` calls. # Version 1.25.1 [2012-04-16] ## New Features * Added support for `fitNaiveGenotypes(..., flavor = "fixed")`. * GENERALIZATION: Now `fitNaiveGenotypes()` returns also `flavor` and `tau`. The latter are the genotype thresholds used by the caller. ## Code Refactoring * CLEANUP: Dropped argument `flavor` of `callNaiveGenotypes()`; it is instead passed to `fitNaiveGenotypes()` via `...`. # Version 1.25.0 [2012-03-30] * The version number was bumped for the Bioconductor devel version. # Version 1.24.0 [2012-03-30] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.10 for R (>= 2.15.0). # Version 1.23.0 [2011-10-31] * The version number was bumped for the Bioconductor devel version. # Version 1.22.0 [2011-10-31] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.9 for R (>= 2.14.0). # Version 1.21.2 [2011-10-10] ## Code Refactoring * Updated `robustSmoothSpline()` such that it works with the new "uniqueness" scheme of `smooth.spline()` in R v2.14.0 and newer. It is tricky, because `robustSmoothSpline()` is a reiterative algorithm which requires that the choosen "unique" x:s does not change in each iteration. Previously, `signif(x, 6)` was used to identify unique x:s, which gives the same set of values when called twice, whereas this is not true for the new choice with `round((x - mean(x))/tol)`. # Version 1.21.1 [2011-06-26] ## New Features * Added argument `aspectRatio` to `plotMvsA()`. It can be used to adjust the range of the `Mlim` argument relative to the `Alim` argument. # Version 1.21.0 [2011-04-13] * The version number was bumped for the Bioconductor devel version. # Version 1.20.0 [2010-04-13] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.8 for R (>= 2.13.0). # Version 1.19.6 [2011-04-12] ## Code Refactoring * CLEANUP: Removed internal patch of `principal.curve()`. If an older version than **princurve** v1.1-10 is used, an informative error is thrown requesting an update. The internal patch is part of the offical **princurve** v1.1-10 release (since 2009-10-04). * Now all methods allocate objects with NAs of the appropriate mode. ## Known Issues * Recent updates to `smooth.spline()` in R v2.14.0 causes `robustSmoothSpline()` to break in some cases. # Version 1.19.5 [2011-04-08] ## New Features * Now `weightedMedian()` returns NA:s of the same mode as argument `x`. # Version 1.19.4 [2011-03-03] # Version 1.19.3 [2011-02-05] # Version 1.19.2 [2010-10-22] # Version 1.19.1 [2010-10-18] # Version 1.19.0 [2010-10-18] * The version number was bumped for the Bioconductor devel version. # Version 1.18.4 [2011-03-03] ## Bug Fixes * `findPeaksAndValleys(x, to)` were `x` is numeric would use partial match and interpret `to` as argument `tol` and not part of `...` passed to `density()`. This problem was solved by placing `...` before argument `tol`. Thanks Oscar Rueda at the Cancer Reasearch UK for reporting on and identifying this bug. # Version 1.18.3 [2011-02-05] ## Documentation * Added paragraphs on how to do affine normalization when channel offsets are known/zero. Same for multiscan calibration when scanner offsets are known/zero. * Fixed broken links to help for `iwpca()`. # Version 1.18.2 [2010-10-22] ## Documentation * Minor clarifications to the help page on "1. Calibration and Normalization". This page is now also referenced in `help("calibrateMultiscan")`. # Version 1.18.1 [2010-10-18] ## New Features * Argument `censorAt` for `fitNaiveGenotypes()` has new default. * These updates were supposed to be in v1.17.7, but we forgot to commit them to the Bioconductor repository before the new Bioconductor release. ## Bug Fixes * `fitNaiveGenotypes(..., subsetToFit = <logical>)` would throw an exception reporting `Some elements of argument `subsetToFit` is out of range ...`. # Version 1.18.0 [2010-10-18] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.7 for R (>= 2.12.0). # Version 1.17.6 [2010-10-08] ## New Features * Now `findPeaksAndValleys()` returns a object of class `PeaksAndValleys`, which extends data.frame. # Version 1.17.5 [2010-10-07] ## New Features * Added optional argument `fit` to `callNaiveGenotypes()` for passing a model fit returned by `fitNaiveGenotypes()`. If not specified, `callNaiveGenotypes()` will call `fitNaiveGenotypes()` internally. * Added `fitNaiveGenotypes()`, which previously was only internal of `callNaiveGenotypes()`. # Version 1.17.4 [2010-10-06] ## New Features * Added `findPeaksAndValleys()` for the `density` class, which then `findPeaksAndValleys()` for `numeric` utilizes. # Version 1.17.3 [2010-09-18] ## Software Quality * ROBUSTNESS: Now `normalizeFragmentLength()` asserts that arguments `fragmentLengths` and `y` contain at least some finite values and specifies the same number of units. In addition, the method also gives more informative error messages in case it cannot fit the normalization function due to non-finite values. # Version 1.17.2 [2010-08-04] ## New Features * Added argument `preserveScale` to `normalizeTumorBoost()` to rescale the calibrated allele B fractions for heterozygous SNPs such that the compression relative to the homozgygotes is preserved. # Version 1.17.1 [2010-07-23] # Version 1.17.0 [2010-04-22] * The version number was bumped for the Bioconductor devel version. # Version 1.16.1 [2010-07-23] ## New Features * Now `callNaiveGenotypes()` returns the model estimates as attribute `modelFit`. This feature was supposed to be in v1.16.0. # Version 1.16.0 [2010-04-22] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.6 for R (>= 2.11.0). # Version 1.15.4 [2010-04-08] ## Software Quality * R devel assumes ASCII encoding unless specified. Added explicit Latin-1 encoding to the DESCRIPTION file to `R CMD check` to pass. # Version 1.15.3 [2010-04-04] ## New Features * Added `normalizeDifferencesToAverage()`, `normalizeTumorBoost()`, `callNaiveGenotypes()` and internal `findPeaksAndValleys()`, which all were moved from the **aroma.cn** package. # Version 1.15.2 [2010-03-12] ## Bug Fixes * The example of `fitPrincipalCurve()` used a non-existing argument name in the calls to `substitute()`. Thanks to Brian Ripley at University of Oxford for reporting this. # Version 1.15.1 [2009-11-01] ## Code Refactoring * Now `fitPrincipalCurve()` only uses the internal bug-fix patch if a version earlier than **princurve** v1.1-10 is installed. # Version 1.15.0 [2009-10-27] * The version number was bumped for the Bioconductor devel version. # Version 1.14.0 [2009-10-27] * The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.5 for R (>= 2.10.0). # Version 1.13.6 [2009-10-20] ## Documentation * FIX: CITATION file reverted to that of v1.13.4. # Version 1.13.5 [2009-10-08] ## Documentation * CITATION file (incorrectly) updated by Bioconductor maintainers. # Version 1.13.4 [2009-09-23] ## Documentation * Fixed a few broken Rd links. # Version 1.13.3 [2009-07-15] ## New Features * ADDED: `fitXYCurve()` and `backtransformXYCurve()`. * Added attribute `processingTime` to the fit object returned by `fitPrincipalCurve()`. # Version 1.13.2 [2009-05-29] # Version 1.13.1 [2009-05-13] # Version 1.13.0 [2009-04-20] # Version 1.12.2 [2009-05-29] ## Code Refactoring * Replacing old HOWTOCITE with a standard CITATION file. ## Bug Fixes * Previous bug fix in `backtransformPrincipalCurve()` regarding argument `dimension` broke the initial purpose of this argument. Since both use cases are still of interest, how the subsetting is done is now based on whether the number of dimensions of the input data and the model fit match or not. See help and example code for `backtransformPrincipalCurve.matrix()`. # Version 1.12.1 [2009-05-13] ## Bug Fixes * `backtransformPrincipalCurve(..., dimensions)` did not subset the `X` matrix. Also, the method now returns a matrix of the same number of columns requested. The Rd example now illustrates this. Thanks to Pierre Neuvial, UC Berkeley for the troublshooting and fix. # Version 1.12.0 [2009-04-20] * The version number was bumped for the Bioconductor release version. # Version 1.11.2 [2009-02-08] ## Bug Fixes * An error was thrown in `backtransformPrincipalCurve()` when argument `dimensions` was specified. # Version 1.11.1 [2009-01-12] ## New Features * Added `fitPrincipalCurve()` and `backtransformPrincipalCurve()`. # Version 1.11.0 [2008-10-21] * The version number was bumped for the Bioconductor devel version. # Version 1.10.0 [2008-10-21] * The version number was bumped for the Bioconductor release version. # Version 1.9.2 [2008-09-11] ## New Features * Added argument `onMissing` to `normalizeFragmentLength()` for specifying how to normalize, if at all, data points for which the fragment lengths are unknown. For backward compatibility, we start off by having it `"ignore"` by default. ## Code Refactoring * MEMORY OPTIMIZATION: `robustSmoothSpline()` is now cleaning out more variables when no longer needed. # Version 1.9.1 [2008-05-10] # Version 1.9.0 [2008-04-29] * The version number was bumped for the Bioconductor devel version. # Version 1.8.1 [2008-05-10] ## Bug Fixes * If the `subsetToFit` of `normalizeFragmentLength()` was shorter than the number of data points, an exception was thrown. The test was supposed to assert that the subset was not greater than the number of data points. # Version 1.8.0 [2008-04-29] * The version number was bumped for the Bioconductor release version. # Version 1.7.2 [2008-04-14] ## New Features * Added `normalizeFragmentLength()`. * Added `normalizeQuantileSpline()`. * Renamed `normalizeQuantile()` to `normalizeQuantileRank()`. * Added `plotXYCurve()`. * Added `predict()` for the `lowess` class. # Version 1.7.1 [2007-11-28] ## New Features * The startup message when loading the package is generated with `packageStartupMessage()` so that it can be suppressed. ## Documentation * TYPO: Corrected a spelling error in the help pages. ## Software Quality * Package passes `R CMD check` for R v2.6.1. ## Code Refactoring * Package now only suggest the **R.oo** package, and instead depends on the new **R.methodsS3**. # Version 1.7.0 [2007-10-08] * The version number was bumped for the Bioconductor devel version. # Version 1.6.0 [2007-10-08] * The version number was bumped for the Bioconductor release version. # Version 1.5.2 [2007-08-10] ## Software Quality * Package pass `R CMD check` for R v2.6.0. # Version 1.5.1 [NA] ## New Features * Added `normalizeAverage()`. ## Software Quality * Package pass `R CMD check` for R v2.6.0 with Rd encoding errors. # Version 1.5.0 [2007-05-09] * The version number was bumped for the Bioconductor devel version. # Version 1.4.0 [2007-05-09] * The version number was bumped up with the Bioconductor release. # Version 1.3.1 [2007-01-15] ## Code Refactoring * Removed code to use **modreg** for backward compatibility with R < 1.9.0. * Added **R.utils** to Suggests field of DESCRIPTION. # Version 1.3.0 [2006-10-03] * The devel version number was bumped up with the Bioconductor release. # Version 1.2.0 [2006-10-03] * The version number was bumped up with the Bioconductor release. # Version 1.1.0 [2006-07-20] ## Significant Changes * Added to Bioconductor 1.9. ## New Features * Added some trial RSP pages. Try `browseRsp()` in the **R.rsp** package. # Version 0.1.7 [2006-06-27] ## Code Refactoring * Made the package truely standalone except from **R.oo**. Previously package **R.basic** was used in some of the examples. # Version 0.1.6 [2006-05-22] ## New Features * Added `medianPolish()` which is much faster than `stats::medpolish()` when there are no NA. * Added `plotDensity()` for list of vectors as well as for matrices. * Added `normalizeQuantile()` for lists of vectors as well as for a single vector of numerics. To calculate the target quantile there is a new function `averageQuantile()`, which is also for lists of vectors. It latter does not support robust estimatation of the average, because it safes memory. * Updated `normalizeQuantile()` for matrices according to the updates in the **limma** package. ## Code Refactoring * Added a namespace for the package. * Added `biocViews` since the package will eventually be added to the Bioconductor project. # Version 0.1.5 [2006-04-21] ## Performance * Minor speedup to `weightedMedian()`, e.g. negative weights do no longer give and error, but are treated as zero instead. This removes some overhead of the function. Also, if it is known that there are no NAs that can be specified by `na.rm = NA`, which will skip NA checks. # Version 0.1.4 [2006-03-28] ## Documentation * Updated broken Rd links. * Updated the references to publications. # Version 0.1.3 [2006-01-22] ## New Features * Now `fitIWPCA()` does not return the data matrix. This is to save memory. The calling algorithm can equally well add the data if it is needed. ## Documentation * Added help on the returned parameters of `fitIWPCA()`. # Version 0.1.2 [2005-09-06] ## New Features * All plot methods displaying log-ratios now assures that no fake log-ratios are calculated due to two negative raw signals. Similarily, methods display log-intensities now assures that the log-intensities are calculated as doubles to avoid possible overflow warnings for too large integers. # Version 0.1.1 [2005-07-26] ## New Features * Added `sampleCorrelations()` and `sampleTuples()`. * Now argument `interpolate` of `weightedMedian()` defaults to TRUE only if `ties` is NULL. # Version 0.1.0 [2005-06-03] ## Significant Changes * Created. Most of the matrix methods were copied from the **R.basic** and the **aroma** packages. The purpose of this package is to provide a standalone package, which does not require any of the aroma classes. This will allow the methods to be used by end users as is, or be utilized in other packages.