NEWS

metadeconfoundR 1.0.2 (2024-06-25)

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

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

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)

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

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

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

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

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

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

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

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