Changes in version 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)
Changes in version 1.13.1 (2022-02-11)
+ update unit tests, e.g. remove ggm for as.data.frame, set R=1000 for bayes
Changes in version 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
Changes in version 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
Changes in version 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
Changes in version 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
Changes in version 1.11.2 (2021-08-30)
+ change error message in test_combine
Changes in version 1.9.6 (2021-08-27)
+ change error message in test_combine
Changes in version 1.9.6 (2021-05-05)
+ reduce dependencies, remove the sna package
Changes in version 1.9.5 (2021-05-04)
+ add functionality to adjust for multiple testing in correlation
+ return symmetric matrices when returning ppm ranges in structural
Changes in version 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
Changes in version 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)
Changes in version 1.9.2 (2021-03-24)
+ add section on structual matrix generation for directed=FALSE
Changes in version 1.9.1 (2021-02-20)
+ fix typos in the vignette
Changes in version 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
Changes in version 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
Changes in version 1.5.2 (2019-12-11)
+ change unit tests for clr and aracne that it doesn't fail in Windows
Changes in version 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
Changes in version 1.3.1 (2019-09-06)
+ change License to GPL (>= 3)
+ add codecov
+ add Travis-CI for continuous integration
+ add CITATION file
Changes in version 1.1.2 (2019-04-16)
+ check that MetNet passes all builds without any errors or warnings
Changes in version 1.1.1 (2019-04-03)
+ correct typo in vignette
Changes in version 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
Changes in version 0.99.23 (2018-10-16)
+ improve createStructuralAdjacency function
Changes in version 0.99.20 (2018-08-06)
+ replace psych::corr.test by WGCNA::corAndPvalue to improve speed
Changes in version 0.99.19 (2018-07-26)
+ print message when model calculation in createStatisticalAdjacency is
finished
Changes in version 0.99.18 (2018-07-19)
+ set rfPermute.formula to rfPermute.default in order to use num.cores
Changes in version 0.99.17 (2018-07-19)
+ set num.cores to 1 in test_statistical for randomForest
Changes in version 0.99.15 (2018-07-16)
+ do not import stabsel from stabs
Changes in version 0.99.14 (2018-07-14)
+ use BiocManager instead of BiocLite for installation
Changes in version 0.99.13 (2018-07-12)
+ do not export functions threeDotsCall and addToList
Changes in version 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
Changes in version 0.99.11 (2018-07-03)
+ speed up function rtCorrection by vectorizing
Changes in version 0.99.10 (2018-07-03)
+ speed up function createStructuralAdjacencyMatrix by vectorizing
Changes in version 0.99.9 (2018-06-26)
+ change 1:... to seq_len()
Changes in version 0.99.8 (2018-06-26)
+ implement function rtCorrection
Changes in version 0.99.6 (2018-06-13)
+ use camelCaps for functions
+ use no spaces between '=' and named arguments
Changes in version 0.99.6 (2018-06-12)
+ fix typo in lasso function
Changes in version 0.99.5 (2018-06-12)
+ change 1:... to seq_len()
Changes in version 0.99.4 (2018-06-12)
+ change 1:... to seq_len()
Changes in version 0.99.3 (2018-06-11)
+ remove sum check for correlation
Changes in version 0.99.2 (2018-06-11)
+ require R version >= 3.5
Changes in version 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
Changes in version 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