NEWS

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metadeconfoundR 1.0.3

• implementation of new funtion GetPartialEfSizes()
• adds partial R-squared as additional effect size metric
• new output column "partial": additional variance of a feature explained by adding a metavariable to a linear (mixed effects) model containing all other metavariables associated to the feature
• new output column "partialRel": proportion of explainable variance of a feature tracable to a metavariable (e.g. partialRel = 0.5 --> metavariable x can explain 50% of all explainable variance of fature y -- all other metavariables significantly associated to feature y can explain the remaining 50% of overall explainable variance of fature y)
• new output column "PartialNorm": proportion of explained variance of a metavariable set in relation to maximally explainable variance (i.e. variance not explainable by all other metavariables)
• bug fix of bug disabling computation of confidence intervalls of lrts
• implementaion of truly linear computation mode when nnodes = 1
• additional test to filter out non trustworthy lrts in some scenarios with highly colinear metavariables
• BuildHeatmap()
• added "plotPartial" argument to choose between
• "marginal": plotting naive/marginal effect sizes based on CLiff's Delta/Spearman's Rho
• "partial": plotting signed partial R-squared, including an additional column showing the total explainable variance per feature
• "partialRel": plotting proportion of explainable variance of a feature tracable to a metavariable
• "partialNorm": plotting respective normalized partial effect size

metadeconfoundR 1.0.2 (2024-06-25)

• CRAN release

metadeconfoundR 1.0.1

• fixes for CRAN resubmission

metadeconfoundR 1.0.0

• CRAN submission

metadeconfoundR 0.3.1

• reduced side effects after interrupted metadeconfoundR runs (tmp file removal)
• bugfix: Qcutoff now correctly used to collect potential confounders from naive associations
• improved initial input data quality control (order, problematic row-/colnames, class)
• minor bugfixes in Buildheatmap()
• added LogLevel argument to change verbositiy of logging

metadeconfoundR 0.3.0

• randomVar argument is now simplified: just supply character vector of metaMat variables to be treated as random effects (e.g. randomVar = c("var1", "var5"))
• NEW fixedVar argument implemented: same usage as randomVar, but adds fixed effect terms to all models
• implemented computational speed-up for datasets with large number of metavariables
• metadeconfoundR is now compatible with Unix AND Windows operation systems
• fixed a bug that lead to an error when a feature with extremely low number non-NA values was present in featureMat
• improved error messaging for an error in BuildHeatmap function
• addition of NEW "rawCount" mode, that runs modelling steps on not normalized/rarefied data by including totalReadCount per sample information into glm/glmer comparisons
• for naive significance test and effect size calculation, rawCounts will be normalized by dividing by totalReadCount per sample
• updated implementation of logistic regression mode: test for association of binary features to metavariables by setting "logistic = TRUE"
• experimental NEW feature: return all computed models alongside normal Metadeconfound() output by setting collectMods = TRUE. WARNING: For now, this only works without utilizing parallel processing in the model building step. Larger datasets might take a lot of time processing.
• NEW BuildHeatmap() argument "tileBordCol" sets tile border color (Default "black")
• NEW BuildHeatmap() argument "reOrder" to turn on/of sorting of features and metavariables in the reulsting plot

metadeconfoundR 0.2.8

• changes in status label names and corresponding plotting behavior
• reversed default color scheme for effect size plotting (red = low, blue= high)
• computation of confidence intervals in model building step now default (with added OK_d label for deconfounded but doubtful associations)

metadeconfoundR 0.2.7

• improved error messages and behavior for no/low number of significant associations
• can now plot results with only a single feature/and or metadata

metadeconfoundR 0.2.6

• fixed bug in legend creation of BuildHeatmap(cuneiform = TRUE), direction of association now labeled correctly

metadeconfoundR 0.2.5

• fixed bug in "keepFeature" functionality of BuildHeatmap()
• fixed bug in BuildHeatmap() that resulted in incomplete removal of features showing not a single significant association
• implemented speedup for runs of Metadeconfound(startStop = "naiveStop") with large number of metadata

metadeconfoundR 0.2.4

• Buildheatmap(cuneiform = TRUE) can now handle NA or zero effect sizes (added NEW symbol)

metadeconfoundR 0.2.3

• fixed bug that only occurred when metadata only has one column
• implemented speedup when startStop = "naiveStop"

metadeconfoundR 0.2.2

• added functionality to BuildHeatmap()
• range of shown effectsizes in using d_range parameter (set to "full" for consistent legend between plots)
• range of colors used to show effect sizes can be changed using d_col
• matavariables and features, that should be kept in the plot even without passing q_cutoff and d_cutoff cutoffs, can be supplied using keepMeta and keepFeature parameters

metadeconfoundR 0.2.1

• added functionality to Metadeconfound()
• output can now also be generated in long format
• added functionality to BuildHeatmap()
• input can now also be read in long format
• "human readable"" names for features and metadata can be supplied in addition to the Metadeconfound() output and will be plotted instead of "machine readable" names
• slightly improved help pages

metadeconfoundR 0.2.0

• NEW function ImportLongPrior() to easily import prior knowledge of feature metadata associations present in the current dataset.
• slightly improved help pages

metadeconfoundR 0.1.9

• bugfix concerning random effect variable behavior
• minor aesthetic improvements in BuildHeatmap() output

metadeconfoundR 0.1.8

• introduction of global parameter "logistic"
• logistic = TRUE: analyzing binary features instead of continuous using logistic regression models

metadeconfoundR 0.1.7

• bug fix in BuildHeatmap function

metadeconfoundR 0.1.2

• critical bug fixed, that resulted in greatly increased "NS" status labeling