NEWS.md

In waldronlab/lefser: R implementation of the LEfSE method for microbiome biomarker discovery

version 1.15.10

• [Major] Name of the two arguments for lefser function is changed from groupCol and blockCol to classCol and subclassCol, respectively.
• [Major] Defunct expr argument in lefser
• [New function] lefserPlotFeat plots the histogram of relative abundance (in the (0,1) interval) of the selected features
• [New function] lefserPlotClad draws the cladogram of the significantly more abundant taxa and their LDA scores
• [New function] lefserClades runs the lefser, returning additional information (e.g., agglomerates the features abundance at different taxonomic ranks) required for lefserPlotClad.
• [New feature] Visualization functions are using a color-blind friendly color palette by default.

version 1.15.7

• [Major algorithm update] We remove the step (createUniqueValues) in the lefser function, which used to add small random numbers to make all the values unique. Potential issues (e.g., LDA) due to excess 0s should be managed by filtering out low abundant features from the input.

lefser 1.15.3

• The column names of lefser output is changed to c("features", "scores") from c("Names", "scores")
• [New feature] The get_terminal_nodes function to select only the terminal nodes of the hierarchical features (e.g., taxonomic data).
• [Major algorithm update] Add an option for adjusting the first Kruskal-Wallis Rank Sum Test and Wilcoxon-Rank Sum test for multiple hypothesis testing through the new argument method in the lefser function.

lefser 1.14.0

• [Error fix] The lefserPlot function merged the duplicated labels when the truncated name of the feature is used. Now those are plotted separately.
• [New feature] The lefserPlot function accepts the title argument that adds the barplot title.
• [Update] The feature names of the lefserPlot outputs are re-positioned for the improved readability.
• [Major algorithm update] Sub-sampling and bootstrap for LDA step in the lefser function is removed. Now the LDA score is calculated directly from the whole samples.

lefser 1.12.0

Significant user-visible changes

• The checkAbundances argument in lefser() checks that data are as relative abundances and warns if otherwise (@LiNk-NY @sdgamboa, #28)
• relativeAb helper function available to convert data (@LiNk-NY)
• Deprecate the expr argument and use relab (short for relative abundances)
• Add group labels to lefserPlot (@LiNk-NY #25, @asyakhl #31)
• 'Interoperating with phyloseq' section added to the vignette (#16)

lefser 1.0.0

• lefser is an R/Bioconductor implementation of the LEfSe method for microbiome marker discovery (https://doi.org/10.1186/gb-2011-12-6-r60)
• LEfSe uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers in groups and sub-group blocks.
• lefser also implements the format of the LEfSe barplot of results

waldronlab/lefser documentation built on Nov. 1, 2024, 9:02 p.m.