Changelog

Source: NEWS.md

MsCoreUtils 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.

MsCoreUtils 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

MsCoreUtils 1.13

MsCoreUtils 1.13.1

• Add functions entropy and nentropy.

MsCoreUtils 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

MsCoreUtils 1.10

MsCoreUtils 1.10.0

• New Bioconductor 3.16 (stable) release

MsCoreUtils 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

MsCoreUtils 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

MsCoreUtils 1.5

Changes in 1.5.1

• Add which.first and which.last.

Changes in 1.5.0

• New Bioc devel version

MsCoreUtils 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

MsCoreUtils 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)

MsCoreUtils 1.0

Changes in 1.0.0.

• Bioconductor release version (Bioc 3.11)

MsCoreUtils 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.