Changes in version 1.19
MsCoreUtils 1.19.2
- Fix reduce() to merge also ranges with the same end.
MsCoreUtils 1.19.1
- Add new reduce() function to reduce overlapping numeric ranges to
disjoint ranges.
Changes in version 1.17
MsCoreUtils 1.17.3
- Use R_Calloc and R_Free instead of Calloc and Free in
src/lowerConvexHull.c, respectively, to reflect changes in the R API
and fullfil STRICT_R_HEADERS check.
MsCoreUtils 1.17.2
- Fix typo in normalisation methods description.
MsCoreUtils 1.17.1
- Fix common_path() to not return also the file name if the input
parameter contains only identical character strings.
Changes in version 1.15
MsCoreUtils 1.15.7
- Add common_path() function.
MsCoreUtils 1.15.6
- Bump version to force new package build on Bioconductor servers.
MsCoreUtils 1.15.5
- Add function force_sorted() to adjust a numeric vector to ensure
increasing/sorted values.
MsCoreUtils 1.15.4
- Fix partial argument match (see issue #125).
MsCoreUtils 1.15.4
- Fix documentation of ndotproduct.
MsCoreUtils 1.15.3
- Add function breaks_ppm to create a sequence of numbers with
increasing difference between elements (defined by parameter ppm).
MsCoreUtils 1.15.2
- Porting baseline estimation function (see issue 119).
MsCoreUtils 1.15.1
- Remove impute_mle2() since norm2 has been removed from CRAN (see
issue 117).
MsCoreUtils 1.15.0
- New Bioc devel version
Changes in version 1.13
MsCoreUtils 1.13.1
- Add functions entropy and nentropy.
Changes in version 1.11
MsCoreUtils 1.11.6
- Fix bug in impute_MinDet(MARGIN = 1) and add unit test.
- Check that package is available and namespace is loaded adding
stopifnot() when calling requireNamespace().
MsCoreUtils 1.11.5
- Add function maxi to determine the maximal intensity value. This
function returns NA_real_ instead of -Inf if all values are missing
or if the length of the input parameter is 0.
MsCoreUtils 1.11.4
- Check if parameter y is increasingly ordered in bin: issue #108.
MsCoreUtils 1.11.3
- Add function sumi to sum intensity values with correct NA handling.
MsCoreUtils 1.11.2
- Reimplement between in C (see issue #105).
- Use symbols to call registered C methods for faster lookup (see PR
#106 and Writing R extensions: Converting a package to use
registration).
- Documentation improvement: explicitly mention impute_mle2() in the
MLE imputation paragraph.
MsCoreUtils 1.11.1
- Add a MARGIN argument to (relevant) imputation functions to support
(and make it explicit) along which dimensions (row or columns)
imputation is performed.
- New impute_mle2() function that uses norm2 (see issue #100).
MsCoreUtils 1.11.0
- New Bioconductor 3.17 (devel) release
Changes in version 1.10
MsCoreUtils 1.10.0
- New Bioconductor 3.16 (stable) release
Changes in version 1.9
MsCoreUtils 1.9.2
- feat: imputation is compatible with HDF5Matrix objects
- feat: normalization is compatible with HDF5Matrix objects
- feat: matrix aggregation is compatible with HDF5Matrix objects
- fix+feat: aggregate_by_matrix now correctly handles missing data and
implements 'na.rm'
- Fix rla/rowRla man page.
MsCoreUtils 1.9.1
- Random forest imputation (using missForest) is now available
(`method = "RF")
MsCoreUtils 1.9.0
- New Bioc devel version
Changes in version 1.7
MsCoreUtils 1.7.5
- Function bin gains parameter returnMids to choose whether or not bin
mid-points should be returned in the result list.
MsCoreUtils 1.7.4
- Fix ppm to always return a positive value (issue #94).
MsCoreUtils 1.7.3
- Add citation.
MsCoreUtils 1.7.2
- Use Matrix::colSums() by default to handle sparce 'Matrix' and
'matrix' adjacency matrices.
MsCoreUtils 1.7.1
- New aggregate_by_matrix() that uses an adjacency matrix to aggregate
quantitative features.
- Set colnames to the outputs of aggregate_by_matrix() and
aggregate_by_vector() to make sure that these are always set and not
reply on the underlying function.
MsCoreUtils 1.7.0
- New Bioc devel version
Changes in version 1.5
Changes in 1.5.1
- Add which.first and which.last.
Changes in 1.5.0
- New Bioc devel version
Changes in version 1.3
Changes in 1.3.3
- Add join_gnps and gnps to allow calculation of GNPS spectra
similarity scores.
Changes in 1.3.2
- Add rt2numeric(), rt2character() and formatRt().
- New impute_fun() function for user-provide imputation function.
Changes in 1.3.1
- Add Josep Badia Aparicio as a contributor
Changes in 1.3.0
- New Bioc devel version
Changes in version 1.1
Changes in 1.1.7
- Rewrite c("left", "right", "inner", "outer") join in C <2020-10-06
Tue>.
Changes in 1.1.6
- Rewrite closest in C <2020-09-24 Thu>.
- Fix #65 and #66.
Changes in 1.1.5
- Add ... to functions to join and compare peaks; see also #131.
Changes in 1.1.4
- Change references to Feature to QFeatures <2020-07-14 Tue>
- Ensure closest accept just argument tolerance of length 1 or
length(x); see also #61, PR #62 <2020-08-07 Thu>.
- The tolerance argument in closest should now be of length 1 or of
length(x) (was length(table) before) <2020-08-20 Thu>.
Changes in 1.1.3
- For an empty table closest and common return a vector of length x
with NA or FALSE, respectively (instead of 1 and TRUE). Fixes #55
<2020-06-18 Thu>.
- closest and common ignore NA in table <2020-06-19 Fri>.
- Fix rbindFill for single data.frame or DataFrame as input
<2020-06-23 Tue>.
Changes in 1.1.2
- New colCounts() aggregation function <2020-05-27 Wed>.
Changes in 1.1.1
- Add some popular distance/similarity metrices: ndotproduct
neuclidean navdist nspectraangle; see also PR #33.
- Add deprecation note to dotproduct <2020-05-22 Fri>.
Changes in 1.1.0
- Bioconductor devel version (Bioc 3.12)
Changes in version 1.0
Changes in 1.0.0.
- Bioconductor release version (Bioc 3.11)
Changes in version 0.99
MsCoreUtils 0.99.3
- Trigger build.
MsCoreUtils 0.99.2
- Provide more comprehensive description.
- Add vignette.
MsCoreUtils 0.99.1
- Additional functions, and using Author@R to specify (unique)
RforMassSpectrometry Package Maintainer.
MsCoreUtils 0.99.0
- First release of MsCoreUtils with core function to get extreme
values, grouping/matching, noise/smoothing, similarity measurements,
various helper function, and function to process (impute and
normalise) quantitative features.