Version 1.0.2 - fixes for CRAN resubmission Version 1.0.0 - CRAN submission Version 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 Version 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 Version 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) Version 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 Version 0.2.6 - fixed bug in legend creation of BuildHeatmap(cuneiform = TRUE), direction of association now labeled correctly Version 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 Version 0.2.4 - Buildheatmap(cuneiform = TRUE) can now handle NA or zero effect sizes (added NEW symbol) Version 0.2.3 - fixed bug that only occurred when metadata only has one column - implemented speedup when startStop = "naiveStop" Version 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 Version 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 Version 0.2.0 - NEW function ImportLongPrior() to easily import prior knowledge of feature metadata associations present in the current dataset. - slightly improved help pages Version 0.1.9 - bugfix concerning random effect variable behavior - minor aesthetic improvements in BuildHeatmap() output Version 0.1.8 - introduction of global parameter "logistic" - logistic = TRUE: analyzing binary features instead of continuous using logistic regression models Version 0.1.7 - bug fix in BuildHeatmap function Version 0.1.2 - critical bug fixed, that resulted in greatly increased "NS" status labeling