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NEWS
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CHANGES IN VERSION 0.4.2
------------------------------
NEW FEATURE
o all methods can now be applied to SummarizedExeriment objects
CHANGES IN VERSION 0.4.0
------------------------------
NEW FEATURE
o 'reading' output format now includes "SummarizedExperiment" (or "MultiAssayExperiment")
CHANGES IN VERSION 0.3.26
------------------------------
INTERNAL MODIFICATION
o biodb packages now accessed directly on Bioconductor
CHANGES IN VERSION 0.3.25
------------------------------
INTERNAL MODIFICATION
o minor documentation update
CHANGES IN VERSION 0.3.24
------------------------------
NEW FEATURE
o normalizing method including the Probabilistic Quotient Normalization
CHANGES IN VERSION 0.3.22
------------------------------
INTERNAL MODIFICATION
o minor code cleaning
CHANGES IN VERSION 0.3.20
------------------------------
INTERNAL MODIFICATION
o code factorization for drift plots
CHANGES IN VERSION 0.3.18
------------------------------
MINOR MODIFICATION
o minor modification in documentation
CHANGES IN VERSION 0.3.16
------------------------------
NEW FEATURE
o inspecting: drift display: mean of variable intensities (instead of median)
CHANGES IN VERSION 0.3.14
------------------------------
MINOR MODIFICATION
o minor modification in documentation
CHANGES IN VERSION 0.3.12
------------------------------
MINOR MODIFICATION
o travis continuous testing
CHANGES IN VERSION 0.3.10
------------------------------
MINOR MODIFICATION
o hypotesting: exact = FALSE in Spearman correlation test to avoid warnings in case of ties
CHANGES IN VERSION 0.3.8
------------------------------
MINOR MODIFICATION
o 'invisible' return in ExpressionSet and MultiDataSet methods
CHANGES IN VERSION 0.3.6
------------------------------
MINOR MODIFICATION
o annotating: update according to the 'biodbChebi' vignette
CHANGES IN VERSION 0.3.4
------------------------------
NEW FEATURE
o annotating: including the 'biodbChebi' and 'biodbKegg' dependencies
CHANGES IN VERSION 0.3.2
------------------------------
NEW FEATURE
o reducing: updating chemical annotations
CHANGES IN VERSION 0.3.0
------------------------------
NEW FEATURE
o reducing: annotating chemical MS1 redundancy
CHANGES IN VERSION 0.2.28
------------------------------
NEW FEATURE
o writing: new 'prefix.c' argument to include a prefix followed by '_' in the 'dataMatrix.tsv', 'sampleMetadata.tsv' and 'variableMetadata.tsv' file names
CHANGES IN VERSION 0.2.26
------------------------------
NEW FEATURE
o reading: detecting 'DM', 'SM', and 'VM' patterns in file names, in addition to 'dataMatrix', 'sampleMetadata', and 'variableMetadata' (without the need for a '.tsv' extension)
CHANGES IN VERSION 0.2.24
------------------------------
NEW FEATURE
o hypotesting: wilcoxon test 'exact' option set to FALSE because datasets contain ties
CHANGES IN VERSION 0.2.22
------------------------------
NEW FEATURE
o gg_boxplot: now returning the vector of outliers
CHANGES IN VERSION 0.2.20
------------------------------
NEW FEATURE
o gg_volcanoplot: label.vc argument to select labeling
CHANGES IN VERSION 0.2.18
------------------------------
NEW FEATURE
o gg_boxplot: label.vc argument to enable outlier labeling
CHANGES IN VERSION 0.2.16
------------------------------
NEW FEATURE
o filtering: can now take into account sample classes
CHANGES IN VERSION 0.2.14
------------------------------
NEW FEATURE
o filtering: now applied on features first
CHANGES IN VERSION 0.2.12
------------------------------
MODIFICATION
o correcting: the median of the feature intensities is now displayed on the graphics instead of the sum
CHANGES IN VERSION 0.2.10
------------------------------
NEW FEATURE
o filtering: filtering out variables with a proportion of max_na_prop.n of missing values or 0 variance (no more filtering in the 'inspecting' method)
CHANGES IN VERSION 0.2.8
------------------------------
NEW FEATURE
o inspecting: filtering out variables with a proportion of max_na_prop.n of missing values or 0 variance
CHANGES IN VERSION 0.2.6
------------------------------
MINOR MODIFICATION
o search_code (for developers): updating example
CHANGES IN VERSION 0.2.4
------------------------------
NEW FEATURE
o search_code (for developers): to facilitate code development
CHANGES IN VERSION 0.2.2
------------------------------
INTERNAL MODIFICATION
o additional check included in 'reading': in case of multiple column with the same
name in sampleMetadata or variableMetadata
CHANGES IN VERSION 0.2.0
------------------------------
MAJOR CHANGES
o renaming of arguments using the 'snake' notations
CHANGES IN VERSION 0.1.66
------------------------------
MINOR MODIFICATIONS
o gg_plots: filename.c argument renamed to file.c
CHANGES IN VERSION 0.1.64
------------------------------
NEW FEATURE
o gg_pie wrapper for pie charts
CHANGES IN VERSION 0.1.62
------------------------------
MINOR MODIFICATION
o vennplot: minor modification of arguments
CHANGES IN VERSION 0.1.60
------------------------------
NEW FEATURE
o vennplot: wrapper from the VennDiagram::venn.diagram functions
CHANGES IN VERSION 0.1.58
------------------------------
MINOR MODIFICATION
o readme: update (annotating method)
CHANGES IN VERSION 0.1.56
------------------------------
MINOR MODIFICATION
o gg_barplot: order of legend elements in case of flipping
CHANGES IN VERSION 0.1.54
------------------------------
MINOR MODIFICATION
o reading: handling messages and warnings
CHANGES IN VERSION 0.1.52
------------------------------
MINOR MODIFICATION
o transforming: handling of zero and missing values
CHANGES IN VERSION 0.1.50
------------------------------
MINOR MODIFICATION
o gg plots: harmonization of the names of the color argument
CHANGES IN VERSION 0.1.48
------------------------------
MINOR MODIFICATION
o reading/writing: handling of messages
CHANGES IN VERSION 0.1.46
------------------------------
NEW FEATURE
o gg_boxplot
CHANGES IN VERSION 0.1.44
------------------------------
INTERNAL MODIFICATION
o dplyr and tidyr packages now imported
CHANGES IN VERSION 0.1.42
------------------------------
NEW FEATURE
o inspecting: overview plot with ggplot2
CHANGES IN VERSION 0.1.40
------------------------------
NEW FEATURE
o gg_barplot
CHANGES IN VERSION 0.1.38
------------------------------
NEW FEATURE
o gg_volcanoplot: internal use of ggrepel for pretty labels display
CHANGES IN VERSION 0.1.36
------------------------------
NEW FEATURE
o gg_volcanoplot function
CHANGES IN VERSION 0.1.34
------------------------------
NEW FEATURE
o transforming: log transformations on non-zero values only (instead of using log(1 + X))
CHANGES IN VERSION 0.1.32
------------------------------
INTERNAL MODIFICATION
o Code cleaning to meet check standards
CHANGES IN VERSION 0.1.30
------------------------------
MINOR MODIFICATION
o Methods documentation now moved to 'allGenerics'
CHANGES IN VERSION 0.1.28
------------------------------
INTERNAL MODIFICATION
o Suppression of ... in internal functions
CHANGES IN VERSION 0.1.26
------------------------------
MINOR MODIFICATION
o Suppression of ... as methods arguments
CHANGES IN VERSION 0.1.24
------------------------------
MINOR MODIFICATION
o Modification of hypotesting doc to pass biocCheck
CHANGES IN VERSION 0.1.22
------------------------------
NEW FEATURE
o Continuous testing with Travis
CHANGES IN VERSION 0.1.20
------------------------------
NEW FEATURE
o Hypotesting: new 'prefixC' argument to prevent overwriting of existing
"variableMetadata.tsv" columns
CHANGES IN VERSION 0.1.18
------------------------------
NEW FEATURE
o Reading: greping of "dataMatrix.tsv", "sampleMetadata.tsv" and "variableMetadata.tsv"
suffixes at the end of the file names instead of expecting filenames identical to these
three strings.
CHANGES IN VERSION 0.1.16
------------------------------
NEW FEATURE
o Hypotesting: renaming of the signifPrintMaxI parameter
CHANGES IN VERSION 0.1.14
------------------------------
BUG FIXED
o Hypotesting: anova in case some features with only missing values in one or more levels
CHANGES IN VERSION 0.1.12
------------------------------
NEW FEATURE
o Hypotesting: volcano plot with ggplot2 (and plotly)
CHANGES IN VERSION 0.1.10
------------------------------
NEW FEATURE
o Chemical annotation with ChEBI identifiers
CHANGES IN VERSION 0.1.8
------------------------------
NEW FEATURE
o 'annotatingParam' function to display the parameters and their default values
CHANGES IN VERSION 0.1.6
------------------------------
NEW FEATURE
o MS chemical annotation with local database
CHANGES IN VERSION 0.1.4
------------------------------
NEW FEATURE
o MS chemical annotation with ChEBI
CHANGES IN VERSION 0.1.2
------------------------------
MINOR MODIFICATION
o update of the new argument names in 'hypotesting' and 'clustering' in the figure from 'README'
CHANGES IN VERSION 0.1.0
------------------------------
NEW FEATURE
o package creation