NEWS

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MetNet 1.17.2 (2023-02-03)

• improve structural function to work with transformation tables that are tibble objects (contribution by Elva Maria Novoa-del-Toro)
• added unit tests for the transformation tibble case (contribution by Elva Maria Novoa-del-Toro)

MetNet 1.17.1 (2022-11-23)

• replace aes_string by aes since aes_string is deprecated in newest ggplot2 version

MetNet 1.15.2 (2022-05-18)

• improve documentation for function correlation and statistical and include information that also ggm can be used

MetNet 1.15.1 (2022-04-27)

• set ci in corr.test to FALSE to speed up calculation of correlation values (function correlation)

MetNet 1.13.2 (2022-03-04)

• add function addSpectralSimilarity and allow to add a MS2 similarity matrix (contribution by Liesa Salzer)
• adjust the functions threshold and combine to be able to deal with MS2 similarities (contribution by Liesa Salzer)
• adjust the vignette to the changes imposed by the new function addSpectralSimilarity (contribution by Liesa Salzer)

MetNet 1.13.1 (2022-02-11)

• update unit tests, e.g. remove ggm for as.data.frame, set R=1000 for bayes

MetNet 1.11.6 (2021-11-24)

• add ggm method in statistical and implement dealing with NA values for partial correlation and ggm
• add (optional) calculation of ranked absolute coefficients in threshold for the top1, top2, and mean types to take into account negative coefficients (e.g. from pearson or spearman correlation)
• remove ppcor package and use psych::partial.r for partial correlation, calculate the t-values/p-values based on the partial correlation coefficients
• use knnmi.all from parmigene to calculate MI scores, remove mpmi::cmi dependency

MetNet 1.11.5 (2021-10-12)

• add assays in structural based on columns in transformations that are defined by the var argument in structural, adjacency matrices of type will be stored in the AdjacencyMatrix object defined in the columns of transformation
• implement structural that it can also calculate mass differences of 0 for undirected networks

MetNet 1.11.4 (2021-09-09)

• shift calculation of as.data.frame(am) in mz_summary
• several fixes of typos in the comments and vignette
• fix rtCorrection function

MetNet 1.11.3 (2021-08-30)

• change calculation of mass differences, use the differences between (M_2+ppm)-(M_1-ppm) and (M_2-ppm)-(M_1+ppm) instead of (M_1-ppm)-(M_1) and (M_2+ppm)-(M_1) for querying against the list of transformations

MetNet 1.11.2 (2021-08-30)

• change error message in test_combine

MetNet 1.9.6 (2021-08-27)

• change error message in test_combine
• reduce dependencies, remove the sna package

MetNet 1.9.5 (2021-05-04)

• add functionality to adjust for multiple testing in correlation
• return symmetric matrices when returning ppm ranges in structural

MetNet 1.9.4 (2021-04-30)

• add font in mz_vis to mono
• split the example on how to use filter in mz_summary from the visualisation

MetNet 1.9.3 (2021-04-28)

• introduce AdjacencyMatrix S4 class, derived from SummarizedExperiment, to store the adjacency matrices. AdjacencyMatrix objects can be of type structural, statistical, and combine
• adjust the documentation and tests for AdjacencyMatrix objects
• add the functions mz_summary and mz_vis (contribution of Liesa Salzer)

MetNet 1.9.2 (2021-03-24)

• add section on structual matrix generation for directed=FALSE

MetNet 1.9.1 (2021-02-20)

• fix typos in the vignette

MetNet 1.5.3 (2020-03-09)

• change tests for rtCorrection, do not use function levels to test for if '+', '.' or '?' is present in the transformation list
• update vignette that formulas are displayed properly

MetNet 1.5.2 (2020-01-12)

• change unit tests for clr and aracne that it doesn't fail in Windows
• change ppm calculation in structural, use m/z of precursors instead of m/z differences
• change unit tests for clr and aracne that it doesn't fail in Windows

MetNet 1.5.1 (2019-12-05)

• rename combineStructuralStatistical to combine
• combine accepts directly the output of createStructuralAdjacency, before the function combineStructuralStatistical accepted a numeric matrix (first entry of the output of createStatisticalAdjacency)
• remove the functions consensusAdjacency, createStatisticalAdjacency, createStatisticalAdjacencyList
• add functions statistical, getLinks, topKnet, threshold with improved functionality for thresholding the statistical adjacency matrices (based on hard thresholds, or top1, top2 or mean consensus matrix calculation according to Hase et al.) to replace removed functions
• rename createStructuralAdjacency to structural
• change vignette to markdown
• add parameter directed in structural to allow for directed networks
• add parameter values to specify if respectively min, max or all values from the corresponding feature pairs (in the upper and lower triangle) should be taken in statistical

MetNet 1.3.1 (2019-09-06)

• change License to GPL (>= 3)
• add codecov
• add Travis-CI for continuous integration
• add CITATION file

MetNet 1.1.2 (2019-04-16)

• check that MetNet passes all builds without any errors or warnings

MetNet 1.1.1 (2019-04-03)

• correct typo in vignette

MetNet 0.99.24 (2018-10-22)

• adjust NEWS file to new format according to ?news: o entries are grouped according to version, with version header 'Changes in version' at the beginning of a line, followed by a version number, optionally followed by an ISO 8601 format date, possibly parenthesized o entries may be grouped according to category, with a category header (different from a version header) starting at the beginning of a line o entries are written as itemize-type lists, using one of o, *, - or + as item tag. Entries must be indented, and ideally use a common indentation for the item texts

MetNet 0.99.23 (2018-10-16)

• improve createStructuralAdjacency function

MetNet 0.99.20 (2018-08-06)

• replace psych::corr.test by WGCNA::corAndPvalue to improve speed

MetNet 0.99.19 (2018-07-26)

• print message when model calculation in createStatisticalAdjacency is finished

MetNet 0.99.18 (2018-07-19)

• set rfPermute.formula to rfPermute.default in order to use num.cores

MetNet 0.99.17 (2018-07-19)

• set num.cores to 1 in test_statistical for randomForest

MetNet 0.99.15 (2018-07-16)

• do not import stabsel from stabs

MetNet 0.99.14 (2018-07-14)

• use BiocManager instead of BiocLite for installation

MetNet 0.99.13 (2018-07-12)

• do not export functions threeDotsCall and addToList

MetNet 0.99.12 (2018-07-12)

• use BiocStyle package for vignette
• remove Makefile
• use BiocParallel instead of parallel, for instance use bplapply instead of mclapply

MetNet 0.99.11 (2018-07-03)

• speed up function rtCorrection by vectorizing

MetNet 0.99.10 (2018-07-03)

• speed up function createStructuralAdjacencyMatrix by vectorizing

MetNet 0.99.9 (2018-06-26)

• change 1:... to seq_len()

MetNet 0.99.8 (2018-06-26)

• implement function rtCorrection

MetNet 0.99.6 (2018-06-13)

• use camelCaps for functions
• use no spaces between '=' and named arguments
• fix typo in lasso function

MetNet 0.99.5 (2018-06-12)

• change 1:... to seq_len()

MetNet 0.99.4 (2018-06-12)

• change 1:... to seq_len()

MetNet 0.99.3 (2018-06-11)

• remove sum check for correlation

MetNet 0.99.2 (2018-06-11)

• require R version >= 3.5

MetNet 0.99.1 (2018-06-11)

• remove bugs that there are no WARNINGS and ERRORs when running R CMD check and R CMD BiocCheck
• reduce file size of peaklist_example.RData
• submit to Bioconductor

MetNet 0.99.0 (2018-05-14)

• implement functionality to calculate statistical models of correlation (Pearson, Spearman), LASSO, Random Forest, Context likelihood or relatedness network algorithm, algorithm for the reconstruction of accurate cellular networks, constraint-based structure learning algorithm
• implement the function create_statistical_network to calcululate the consensus matrix from the different statistically-infered networks
• implement the function create_structural_network to calculate molecular weight differences and create a network
• implement the function combine_structural_statistical to combine the structurally-derived and statistically-derived network
• implement model partial and semi-partial pearson/spearman correlation using the ppcor package